You can't fly .. (no a real problem, but seriously flying is fun)
You can't create your own spells (but you get shouts instead)
Racial bonuses are not as good
No sign or class bonuses - but get to choose a Stone which makes up for one of them but not both
No Goldbrand/Eltonbrand or Umbra (that I have seen) ..
End Game .. In every other TES game I could get every 'perk' by levelling all skills to 100 (even though this takes forever) .. here you can only get a certain number of them so I cannot be a bada$$ fighter/thief/ranger/all around mage .. I have to choose and specialize (which I actually like, but you are definitely not more powerful)
If you do not specialize in smithing (or if you don't level it to 100 and get the double enchant perk) you get less 'stuff' to enchant and wear ..
The best out of the box (unique and daerdra) armor and weapons are not nearly as good as previous games ..
In the end a specialized character may be better, at the beginning and middle of the game, but by the end of the game its even at best for a specialized character and less powerful for a jack of all trades