Can't speak to THAC0 and Non-Weapon Proficiencies, never having used either, but the other two are to me features rather than bugs: they're good examples of using appropriate tools for different jobs rather than trying to shoehorn everything into one mechanic.
Thief skills being d%? Absolutely - allows for far more granularity than a simple d20. (ditto for various other things that use d% e.g. system shock rolls)
Saving throws? Absolutely - along with what class and level you are and what stats you have, what you're specifically saving against makes a difference in such a system - it's an added variable. One of these days I'd like to expand this further - maybe go to 8 or 10 different types of save rather than just 5 (e.g. split out Poison, Paralyzation and Death into their own charts rather than have them all the same).