This is sooooo off-topic ... but I'll just answer this one.
I think you are reading this as "you get a 3% discount on what you earn after the first 1ME".
The way it's written however (or at the very least what I meant) is "if your income is above 1ME, you get a 3% discount on your whole income": Most tax systems do not work this way, because they try to avoid "hiccups" whereby the extra penny earned suddenly makes you a lot richer or poorer, but situations like this do come up occasionally.
Incidentally I think the Virtue's name should be Less Flawed Magic 
You have a point in that there is little benefit in raising a language to 7 where the affinity starts to pay off, and that therefore a linguist at 50% would not be completely overkill.
OTOH. There is a case for raising masteries to 7+, ten-fold multicastem of Pilum of Fire seems to be popular with some players, and the boosted penetration may come in handy too. Hence an affinity with any mastery is more powerful than an affinity with any language.
Anyway, custom virtues are best designed to be consistent with existing virtues. Revamping the existing virtues should be a separate discussion.
What is consistent though? The new custom virtue being like linguist at 25%, or the new virtue being 50% like nearly every other magic based affinity?
As others pointed out in the first replies, each affinity applies to one ability/art. Linguist and flawless magic are the two examples applying to a class of abilities. Linguist gives 25%. Flawless is major and hence irrelevant.
Nobody has object that masteries are very different from languages. The response has been that maybe linguist is underpowered ...
And I think we can agree that even though Linguist may be underpowered, spell masteries can potentially provide a bigger benefit than languages (for magi et least).
The benefits of an Affinity and something like Linguist cannot be evaluated the same way.
So overall I would maintain that a 25% bonus over a class of abilities is just as useful as a 50% for a single ability. Of course, it takes a bit longer before you reach the 50xp treshold, but over the long term you will get more out of the virtue than from an Affinity.
I disagree. Flawless Magic is the most relevant Virtue to compare to, because it's the only one that specifically offers Spell Mastery xp "over time" (instead of a lump sum at character creation like Mastered Spells).
For 3 Virtue points, FM provides:
a) 5xp for free with every spell learnt.
b) a 100% bonus to subsequent xp spent on mastery.
Unless you claim that benefit a) alone is worth less than a Minor Virtue (and I think nobody would claim that), then benefit b) is worth no more than two Minor Virtues, and at half-strength (a 50% bonus) it is worth no more than a Minor Virtue. A quarter-strength benefit b) providing a 25% bonus is clearly worth less than a quarter of FM, most likely no more than a sixth, so it's clearly underpowered as a Minor Virtue.
As for the benefits from spell mastery vs. affinity, you'll have to ask: without any V&Fs, what fraction of his time does a magus specializing in formulaic spells spend on spell mastery? What fraction does a magus specializing in one or two Arts spend on his best Art(s)? The answer is obviously fuzzy, but I contend that if we looked at a number of real magi from your sagas on average the latter fraction is at least as large as the former. Thus, an Affinity with (Art) is at least as good as an "Affinity with spell mastery", and the latter (a 50% bonus) should again be worth no more than a Minor Virtue.
Going further that road one could count the xp/seasons saved.
You prolly aim at score 20 when you take Affinity for an Art. That 210 xp is reduced to 140 xp with Affinity, saving 70 xp. An early score of 14 is half of that.
Spending the same 210 xp on various masteries would require 42 seasons of practice. With a 50% Affinity bonus, that would be 28 seasons.
How likely would someone other than Flambeau spend 7 years refining spells?
I think counting in Practice seasons miss the point that books can be bought, and that the most common source of spell mastery XP is likely to be aventures anyway. If this was my gaming table, and a player wanted an affinity for all spell masteries for 1 virtue point, I'd allow it, but I probably wouldn't allow stacking with Flawless Magic on top.
At the end of the day I think the point is moot anyway. If you really want to spend 210+ xp on masteries, wouldn't you take flawless magic anyway? Commonly considered overpowered and spot on for your needs, wouldn't effectively be an obvious must-have?
None of the affinities are worthwhile if you do not minmax the character, and maxing out masteries requires flawless magic, so how would you make a minor virtue worthwhile for those who do not maximise masteries to the point of wanting flawless?
Yes, I agree that certain Virtues/Flaws should not combine, Like Faerie Blood and Greater Faerie Blood, or two Magical Focii.
Hence why I named this placeholder for this potential Virtue as "Lesser Flawless Magic".
Not that some Virtues/Flaws can't interact and cause stacking or cancellation. I will have to investigate the "Independent Study" mentioned earlier.
Regarding Independent study:
Minor general virtue.
It increases adventure xp by 3 and practice xp by 2.
Those are the most common ways to acquire mastery (the 5xp/season is via practice)
If you want to look it up yourself, it is from the Merenita chapter of HoH:MC
Nitpicking time. It increases the Source Quality of Practice or Adventure experience.
That is an important difference if the character also has an Affinity or similar.
For 90% of the characters... Yes. Except there's a restriction to one major hermetic virtue. And I can think of characters where Spell Mastery is core to the concept, but not core enough to skip that other Major I want.
Opportunity cost matters. A 25% boost, as mentioned previously, would require 200 XP spent before it begins to be better than the virtue that delivers 50XP at character generation. It takes a lot of seasons to get the XP to begin to be better, and for all those seasons one is catching up, they are a weaker character. If the character design is about mastery, it's hard to say your design is all about mastery, when the character is 50XP behind the other guy who got the virtue.