Funny, a lot of things that I like about 3.5e are what a lot of people don't. I must have terrible taste.
Weapon sizes: I disliked the 3.0 weapon sizes because Small races that would benefit most from Weapon Finesse could only use that feat with the dagger and a few other exotic weapons. Now, a halfling can use a rapier appropriately sized for him.
Square spaces: Rectangular spaces seemed really odd to me because it implied that creatures only ever faced one way in a fight, even if they were attacked from the side or the rear. Square spaces fit better with the concept that creatures turn every which way in a fight to strike at and defend against opponents on all sides.
Summon Mount: A paladin's god gives his champion the ability to summon a helper whenever and wherever he needs it, and people complain? So what if it's never been done before? It's a great idea, and even lawful good gods can innovate, you know. If it makes you feel better, have the paladin transform his pet dog into a dire lion or something.
The whole golf bag of DR issues: I liked the lowering of DR values so that it is now difficult but not impossible to injure a creature when you don't have the right weapon. I'm happy with the existing special materials and alignments. I will start to get annoyed if other special materials are added. I will make an exception for byeshk in Eberron because I like Eberron. Yes, that's terribly biased of me.
Gnome bards: In my own campaign, I was cracking my head over how to give gnomes more of a niche, and decided to re-invent them as a race of fun-loving tricksters whose favored class was bard instead of illusionist. You can imagine how delighted I was when 3.5e was released. Yes, this is another example of personal taste.
And now, back on topic. Things I didn't really like about 3.5e:
1. Needing to be a spellcaster to use Craft (Alchemy). I can see why some of the semi-magical substances need spellcasting ability, but it seems to me that anyone ought to be able to distill acid.
2. The buff spells may have been over-nerfed. 10 mins./level sounds good to me.