Inconsistent and arbitrary rules don't bother me in isolation, as long as they serve some purpose. For example, the racial level limits and race/class combinations in 1st ed. AD&D are arbitrary, but they don't bother me--usually--all by themselves. Rather, it's that, stacked with the initiative system, plus weapon restrictions by class, yada, yada, yada--that starts a slow nag that eventually bothers me. Having all elves be fighter/mu in Basic, in contrast, doesn't bother me--because that is part and parcel of its simple charm. It's elaborate expansions that try to keep vestiges of that assumption (sometimes inconsistently) that bother me--a little. 3E favored classes, for example.
Some of the 1E/2E spell list restrictions seemed rather arbitrary to me. Details escape at the moment, but I'd be thinking "cure light wounds" to cleric makes sense. Yep. Now, "hold person" being lower level, can kind of see that. And then there would be some spells where I couldn't readily fathom a rationalization.
I think 3E/3.5 crafting rules are inconsistent with the rest of the system, and thus they always feel tacked on to me. I was never entirely satisfied with spell lists, either. (I liked Arcana Evolved"s unified spell list far better.)
For 4E, put me down as another one bothered by the precise but arbitrary nature of the rogue weapon restrictions. I'd have liked another descriptor on weapons as useful with a sneak attack, as one possible alternative. I don't care for some seemingly arbitrary feat prerequisites, either.