There is a lot but I will focus on a few.

1.Rage mage
Oh, it could have been sweet. But it being a half-progression PRC just makes it a little less than helpful.

2.Bard
It's cool, but I really would have appreciated full spell casting. It being that master of none type of class isn't a good thing at all. Especially seeing classes like the beguiler and even factotum (which got ALL skills and all wiz/sorc spells (even though they can only cast an extremely limited number per day)
I think it's perfect in 5e though.

3.Assasin.
It has useful spells, but I think it could have been condensed into a 5 level class. That would have made it SICK. And maybe letting up on the pre-requisites.

4.Erudite.
Probably one of my favorite classes. The problem I have is the lack of clarity with the Unique powers per day.
If it could have been 1 per level that would have been perfect.

5.Core melee classes
obviously. They all needed martial maneuvers. We just didn't know until they came out with them.

6. Paladin
I hate the paladin. At best, it should have been a variant class for cleric. more trouble than it's worth.

7.wizard
The spell book mechanic I don't care for. It would have been cool if they just had the opportunity to learn from scrolls, but didn't actually need a spell book or forgot all there spells every day. Spellbooks then simply become a vehicle of transferring knowledge between them. Just as a professor can learn a formula, but uses a math book to help spread the information.