When I read the 4th edition Wizard's Grimoire, I was fascinated by the rules concerning the creation of a homonculus, a sort of magical creation of sentient life using the mandrake root and plenty of the magus' blood. How do you think this would work in 5th edition? Maybe more like the fertility ritual from ancient magic? Let's see some ideas about how to impliment this process in the new edition.
We kind of already have the rules for that. The rules for Awakened Devices allow any material to be used and "awakened". Blood and Mandrake root? No problem! Why those materials? The personality is formed in part by what you use.....
Awakened Device would be adequate, but the homonculus becomes a child which then grows. In the Grimoire, it was a CrCo level 70 ritual with a vim requisite, and which also required the magus to give up a stamina point. This isn't just giving the material sentience, it's essentially making a magical little clone of youself. Then there was the whole alchemy-style process of integrating materials to affect its traits... Awakened device would work, but flavour-wise it seems like it just needs something different. Maybe tweak it to fit with similiar alchemy rules?
Yes, but the Homonculus was never truly alive, as I recall. As to the "little magic clone" of yourself, If you make the Awakened device, you can turn it into your familiar, and as it requires a magic item to awake, why couldn't you turn it into your talisman as well? Between the two, it would be closer then a child, and easier to teach as well.
I say just call it a unique minor Mystery, not dependant on anything else. A "curious common magic" sort of thing.
Which one?
depending upon how hard it is appropriate to make the character work within the confines of the overall plot I might give the character access to books describing the Homonucleus as a full integrated discovery (easy) or make it a minor mystery that could be initiated through an alchemy focused mystery cult (moderately difficult). I don't think that the mini-me secret s sufficiently powerful to force the character to work harder for it, if you do that you'll never see it in the game and everyone losses out.
I mean make it even easier than that, not tied to any line of mysteries at all. The Homonculous is a Minor "Hermetic" Mystery. Any magus can self initiate it with an appropriate script. The Script would include the ordeal of loosing a point of Stamina, plus one or more quests involving the acquisition of the needed materials.
Or just say any magus can already do this if their Arts are high enough. This was integrated centuries ago, just not widely publicized.
Yes, but magic does get lost. We have the rules from Ancient Magic. Use them. Nothing is stopping you from setting the breakthrough at five or ten points. Then you have a story and the player has rediscovered something he cares about, without it taking the game over. I don't think any campaign in Ars Magica would have a problem with a one to two year project.
Also excellent 
Add the question of "why was it lost?". Without reference material for other homonculi, how will you know if yours is deviant or just acting normal. What if he looks just like you, but has a totally different personality? Or perhaps some special knowledge you never taught it?
Did you inadvertantly give flesh to a demon? Or another sort of spirit?
Going off of what is in the Grimoire, it's not a clone in the "copy of you" sense, but in the "it grows up to look like your twin" sense. It doesn't stay small, and is indistinguishable from a normal human after the first month or two aside from its magically improved statistics. So it's not like a little mini-me, it's like growing a child in a magical petri dish.
Check out the section on Homunculi Wizards from Realms of Power: Faerie for another option.