Oh, a few things...
1 - Without animals D&D would be way too boring for any of us. We rather have everyone get a familiar/companion option than just a few classes. My fav bard and his dog are a great team. So are my barbarian and her war elephant.

Of course we changed the familiar rules quite a bit, too.
Changing this cut down the annoying need of having to play druids or wizards to have a companion animal.
2 - Vancian magic. I may not have said it often enough, so here it goes again. It's the one most frustrating, nonsensical, super annoying, boring thing D&D ever made.
3 - Super-multiclassing. As someone else mentioned before. Classes must make some sense together.
4 - Nonsensical treasure - why do monsters have wands, staffs, potions (which don't seem to ever go bad) and the like? Why do some monsters have stuff that's considered treasure by humans, at all?
4 - Badly placed monsters in commercial adventures. Sometimes it would have made sense to read the monster description to know they couldn't be in the climate they were put in!
There are probably a few other things, but that's the most of it. Luckily, All of it was and is adaptable with house rules.