Skills from rare items is sort of why SD3's class change system bothered me. I like abstract systems as much as I like... less abstract ones, but... well, you all know what Nintendo logic is.
Learning skills from items didn't really bug me in FFIX or FFTA. Then again, skill systems that don't really make sense is sort of an FF trademark. Although, FFIX's system WAS a sort of awkward half-way step between the less abstract ideas behind Espers, GFs, and Materia (which were, in a sense, different kettles of the same fish. Or something like that) and the more abstract ideas of, say, license boards and sphere grids.
Granted, I must say that I prefer more straightforward skill systems like in Fallout or something. FFV/FFT had pretty straight forward skill systems via the whole class-based gameplay thing. Pick skill tree. acquire/buy skills. Nothin' strange.
Granted, materia, GFs, and espers had the whole Pokemon/collectibility thing behind them, which is always fun.