I mean I wouldn't say it's unachievable completely; he will be more than capable of doing the research, it's just that nobody will read it and he'll get no respect while he's trying. (Maybe if he eventually gets to a breakthrough he'll finally be vindicated.)
Also occurred to me that needing to do research on the Gift in a small covenant will be a way to get him out of the lab, too, to try out things and see how they work.
I meant "unachievable over the course of the saga".
From experience, the normal pace of a PbP saga is fairly slow, which means any kind of Original Research is unlikely to be completed. A Minor Breakthrough requires about 10-20 years of dedicated experimentation (at least 2 seasons a year) to achieve. The highest pace I have experienced in PbP so far was 1 year of real time for 4 year of game time.
So, again I am simply asking if you will enjoy that concept for that long, considering the many obstacles he will face before he gets any positive results from his research.
Oh as to that it's no problem. I realize the research would just be a backdrop, and probably never achieved, that's true for any player research projects in anything but a fast saga.
Then by all means, go for it! 
Iâm obliged for the magical focus clarification; that would have been an unpleasant oversight!
With the flaws I certainly see some of your points. If we assume that the ghost embodies the nature mysteries goal, and will act as a mentor where appropriate, then both the mentor and the driven flaws can go. Since the higher purpose (of investigating the disappearance of House Merinita and restoring them if practical) is a distinct goal, I feel that this could be retained. I must point out that while the subject matter is related, it is not the same, since there seems no likelihood that the nature mysteries were implicated in the mass disappearance (?!). Furthermore the resolutions are potentially in distinct conflict (e.g. if the original mystery is rediscovered, it may well be that the restored Fae Merinita reject it, and if that version of Merinita remains absent, the Order resists the creation of a new (revived old) Merinita tradition anyway, leaving the options of founding a new cult for this mystery or possibly a new lineage in the event of a suitable breakthrough (if I have that path right). My point is that there is pretty clear potential for further conflict (story material) arising from almost any two possible solutions of these two objectives, and nobody apart from the character is currently interested in both at once.
Going to need at least one more flaw, ideally something to provide a poor reputation for his unfashionable interests; would hedge wizard do, or is that as inappropriate for a Bonisagus as I suspect?
To the other virtues.
I apologise if the reason for Mentem was unclear. The character has suddenly gained a ghostly companion with whom neither he nor his parens is entirely comfortable; both foresee the possibility of future conflict. The logical response was to prepare the character for such a conflict by providing some training in Mentem, as this is I believe the Art used for controlling or resisting spirits. I reasoned that Deft Mentem would be both apt, because it would mean the ghost (of a magus?) might not realise such magics were being prepared against them, and feasible because the character had already demonstrated the ability to be Deft with another Form.
Mentem also broadens the characterâs abilities when dealing with mundanes, where a focus on trees would not be much use at all. There are a lot of situations where a dedicated tree-speaker would not be able to do much, so as you indicate, breadth of capability is useful.
Since his parens is already teaching several specialisms (In, He and spell mastery) and now Me as well, I can see a case for losing Skilled Parens; he wouldnât have time. However, such demands could equally explain this virtue.
I feel obliged to clarify that I thought Well-Travelled xp could only be spent in a limited set of skills of no magical use, including Area Lores, languages, and a few social skills(?) so I really do not see this as narrowing the characterâs focus in any way, rather the reverse.
As I believe that two affinities are explicitly permitted by the core rules, it seemed reasonable to take them. If you really prefer it, I can turn one of them into Puissant, or lose one and retain Skilled Parens. (Indeed, the forum posts Iâve seen suggest that double affinities and double puissance in a given TeFo combination are not unusual, with it being an oddity not to take Skilled Parens.) However unless the trees are both secretly running everything and rather gullible, InHe doesnât seem to be a recipe for powergaming!
That leaves spell mastery, which again provides xp for a very limited use, and in this case has been added deliberately by his parens to intelligently moderate the impact of a flaw. I deliberately did not choose Flawless Magic (a theoretically infinite source of xp!) because I find it unappealing; too powerful and convenient, and also because this could not reasonably (IMO) be taught, but only arise from innate talent.
Rework pending.
Flaws
Twilight prone major hermetic
Plagued by Supernatural Entity (ghost of a Mendalusâ follower?) major, story (Recover the original Merinita nature mysteries and establish a means to preserve them?)
Higher Purpose (Investigate what happened to House Merinita for the good of the Order which is incomplete without a thirteenth House, and rescue/restore if possible or even replace House Merinita with the original version of themselves?)
Hedge Wizard (witters on about House Merinita, thinks declining vis may be a plot too) - maybe Obsessed covers this better?
Slow caster (goes with Cautious Sorceror)
Cyclic Magic (negative, Autumn & Winter)
Virtues (The Gift, Hermetic magus, puissant magic theory)
Major magical focus (trees)
Affinity, Herbam
Skilled Parens
Well Travelled
Cautious Sorceror
Deft Form, Mentem
Mastered spells
Social contacts (mystic forest-dwellers, met while traveling; faeries, foresters with supernatural virtues, cunning-folk, Herbam magi, peregrinatoresâŚ)
After thought, dropped one Affinity for something more social, and tinkered with the flaws some more.
I'm fine with keeping both the ghost and Higher Purpose (though what you describe sounds more like Driven). They are different enough to provide value.
I would comment that the ghost says he was a follower of Mendalus. He could be saying the truth, but he might also be lying about his identity or even his nature. 
Hedge Wizard is definitively out for a Bonisagus. Alternatives would be Infamous and Judged Unfairly. Inafmous would require a severe incident or a series of smaller ones to crystalize your bad reputation, but perhaps it is just that several Bonnisagi believe that your ghost may be tainted by the infernal.
This clashes with my understanding of how virtues are gained during apprenticeship.
There are three types of Hermetic virtues provided by apprenticeship: the House virtue (which is passed on after at least 10 seasons of training), inherited virtues (you had a natural aptitude with some sort of magic at birth and they were shaped when your Gift was opened to Hermetic magic) and virtues taught by the master (your master initiated you in a special kind of magical talent).
A master can only teach a virtue that he has (through a process very similar to a mystery initiation). So your master would have needed to have Deft Mentem in order to teach it to you. And he waited until you had a ghost t do it? Seems a bit far-fetched.
Anyway, there is nothing wrong with the virtues you selected. I simply see a stacking of several virtues that give more xp, so that your starting Arts and Abilities can be higher. For the moment, it looks like a shortcut for power on paper, but less colorful as a character.
I just have trouble seeing how it all comes together because I am not seing any background for the character. Can you tell me more about your magus as a person? His history and background? That is where the stories come, not the stats. 
John, I think it's worth pointing out that Vim is just as good as Mentem for dealing with ghosts, and has applications to faeries and other supernatural creatures too.
I was planning on making my researcher a Mentem specialist so it might be nice not to overlap, too. But I don't really mind if we both are if that's what you prefer.
Arthur, do you have an issue with magi taking Magister in Arbitus?
That is a difficult one to integrate for a Bonisagus. Your studies as a Magister would need to be completed before you were taken as an apprentice (so older than 35, with no Longevity Ritual), have Gentle Gift, and a very good background explaining why he's not in House Jerbiton.
I am tempted to just say no. Just not suitable for this saga.
We can just go with no, that's why I checked. Different SGs handle the time aspect of it differently.
@Arthur Working on personal history; what do you think is the latest a gift and the negative effects can show up? Or is the negative part from birth?
Thinking of a noble being educated who suddenly found that everyone hated him. Parents sought a "cure" which led to him being apprenticed. All of which led to him wanting to tackle the gift as a problem.
From Apprentices p.21:
The Gift reveals itself in several unpredictable ways. Sometimes it is evident at birth, other times it is triggered by puberty or an early traumatic event.
So any time between birth and age 12 is fine. Older is not impossible, but highly unusual.
I was intending maybe enough InMe (mostly In) for Posing the Silent Question before starting to think about anti ghost effects and form bonuses. Since itâd be a very rare Bonisagus with a low Vim, I could shift to Vi instead of Me so long as the SG concurs itâs a reasonable choice for a parens to make in the circumstances. Settles the issue of the Deft virtue as wellâŚ
Vim is certainly more versatile for the kind of investigation you are likely to do, as it will help investigate former Merinita sites, protect yourself from faeries, etc. It can also be used to ward against or destroy a ghost.
However, Mentem remains a better overall form when dealing with ghosts. It is simply more flexible when dealing with a person's mind (dead or alive) and emotions.
Note that spells dealing specifically with ghosts (wards and such) need to be Realm-aligned, whether you are using Vim or Mentem.
But yes, a Bonisagus master would probably steer his apprentice towards Vim, unless that master was a ghost or Mentem specialist.
I was also considering âfollower of Merinitaâ but canât recall why I didnât use it -someone with a connection to the nature mysteries anyway.
Infamous would require some significant bridge-burning, and Judged Unfairly is too general. The game effect of Infamous Master would work, but the reasoning doesnât fit. Obsessed is near the mark but not quite deep enough. Argh!
Iâll pencil in Infamous, as I can at least think of a way to make that occurâŚ
Understood. I have some thoughts about background, but theyâre rather mutable at this stage, and as they develop, so the stats change. For example, I started out thinking his family would be some combination of foresters and cunning-folk, except that the forester angle suggests some martial abilities (for opposing poachers etc.) and I wasnât looking for a combatant. The cunning-folk link is important though, because I was thinking thatâs how his master found him. This suggests some supernatural talent in the mix, currently thinking of visions and/or premonitions having manifested before his master found him (fits with an Intellego specialism), with other latent talents able to be reshaped into the Major focus.
I briefly considered woodcutter instead of forester, but using an axe is close to martial abilities again (though technically a craft?) and also doesnât sit very well with being interested in trees for their own sake (unless he actively rejects that aspect of his own background, which could actually make this viable!).
I was most recently thinking of a family background as timber merchants, which is rather less humble, but fits very nicely with well-travelled, but am now thinking of woodcutter againâŚ
If you want him to have some background in the wood industry, here are some samples:
Millworker (the people who turn cut trees into beams and boards)
Carpenter (Making houses and furniture)
Grove-keeper (They tend to a grove of tress, so that no one poaches them, and to make sure they produce fruit)
If you want something that's good for trees, and yet moves around, you might want a bee keeper, as the hives need to move to pollinate a variety of plants/trees.
Thank you! I am aware of Gwydion in MoH, the tree and bee specialist, so I was trying to differ from that example a bit, although I suppose a little Animal wouldnât hurt. However, a minor magical focus in bees would be a shift in emphasis for sure, but an idea to remember for another time.
Carpentry would likely result in a craft guild link for the family at least, although as skilled craftsmen carpenters could occasionally travel too, so long as they were skilled enough to be hired for significant projects.
Grove-(or orchard?) keeper would also be a passable fit.
Millworker would be rather removed from the trees, and also settled, not to mention visible to nobles (who would often own, or at least personally issue a charter for, a mill).
Indeed there is some crossover between some of these trades; maybe he has brothers and uncles in such trades! Purpose built beehives with removable frames would require a skilled carpenter to build, after allâŚ
For a variety of reasons, including my creative difficulties, I'm going to withdraw and let my spot go to someone else.
Sorry to hear that!
Thank you for telling us.