If there is in fact in the realms of 180 perks as was suggested, I'm willing to bet that some of these will be what we typically associate with lore skills. For an alchemist, there could be herb lore (as a perk), which enables you to identify the names of the plants. Later you can get the alchemy lore perk, which allows you also to recognize the effects simply by looking at the plant. Before you get there, you might have to carry around recognition books. How about language lore? Once you get it, you may be able to read foreign languages, where books are decrypted on the fly. Or spell lore, in which you cannot identify new scrolls you find out in the wild. Listed in inventory simply as a Scroll. Cast it on a foe and it turns out it was just some Open Lock scroll. Memory perk, where said scroll will be memorized if you cast a Scroll you didn't have identified, so that next time you find an Open Lock scroll, you will be able to identify it since you have its letters memorized.
So there are many ways these perks can make the game just that little bit easier. For some of us, it's not about making the most useful set of skills to make us most efficient (the game adjusts anyway, right?), but having perks that defines who we want to be. Perks that are useful to Hoblak the Librarian may be useless for Badprenup the Barbarian, but don't claim anything to be useless because they are to you. Pick a lock bashing perk instead of a scroll identifying perk if bashing better suits your character. Role Master (dice game system) had several hundred skills, of which most was "useless" for most. But a good GM would recognize these skills being picked and adjust his campaign to suit so they became useful. Want in a door? Thieves around? Lock it with a common lock to be picked. Any mathematicians around? Make them apply advanced math to break a code. Only fighters? Sorry guys, it can't be bashed, it's solid steel.
Coding it for a computerized GM? Yeah, *that's* the tricky part