I learned of this since I transferred over the shiny beasts and Celebi.
You can't transfer your items.
That is the one thing that annoys me the most, because I have to start from scratch as far as getting the EV items and collecting all the berries.
Another thing is the bag, how it's all disorganized. Yeah, sure, they still gave the key items, berries, and TMs/HMs their own bags, but they could have put the pokeballs in their own instead of shoving them in with the main bag. :/ I also liked organizing the items the way I wanted them instead of how the game organizes it, which is held items first in alphabetical, then random items in alphabetical, then pokeballs in alphabetical. Dx
Oh, and the ginormous level jump after the E4. I'm fine now, but holy crap, I literally had to go to a Pokemon Center after every battle/encounter.
I won't even get into the names.
I miss the item PC. I hate having to carry around EVERY. SINGLE. ITEM. I. FIND.