Well, since this thread is not about what 3.x does better than 1E, but about what I disliked about 1E, I will have to say:
Armor Class - I always wanted AC to be like it is now
No Skills - I started to add NWP's from the survival guides
Level Limits on Non-humans - Just seemed wrong
Bards - yuck
Psionics - worse than Bards... never used them and still don't
Weapon Restrictions by Class - Yes, I know it was there for balance
Fire and Forget Spells - Still hate this one in 3.x
I didn't mind the charts and had almost all of them memorized. I could calculate XP on the fly or whatever, because I looked at the chart so often at first. Now, I look at some rules so infrequently that I forget and have to re-read the core books. Of course, then I played almost every day, now I play almost every week.
The adventures were amazing and still are. Most of the players I know who never even played 1E or that were not even born yet hold them in reverence if they have played them. Very few "new" adventures hold up to that standard. The best adventures for 3.x (IMO) are by Necromancer, some of the WOTC adventure path adventures (though some of those were real stinkers, so it balanced) and the contents of the last 8-10 or so Dungeon Adventures magazines (for the most part).
DM