First, to comment on things people have said already:
- True, in your bag, you can organise your items so the most important ones are on top. The problem is, if you give an item to a Pokemon then take it back, it appears at the very end of the list in your Bag. I have several Arceus plates in my bag and keep alternating them between my Pokemon, so this is really annoying.
- The mud in the Great Marsh isn't hard to get through if you get stuck. Just turn around in a circle and you'll come right out. In the Great Marsh it's actually a plus to get stuck in the mud because it allows you to stay in one place for a few paces, thus extending your time. Whenever I go into the Great Marsh, I look for places to get stuck in the mud.
And some new complaints:
- The appeal round of Pokemon Contests was better in R/S/E in my opinion. If only they could just replace the final round of the Super Contests with the final round of the original Contests, that would be perfect. The thing that really sucks about the Super Contests is that you can't take points away from other Pokemon, and you can't Startle or Unnerve or boost condition. Plus, three judges makes it both confusing and hard to get the crowd going.
-There's no way to reverse the effects of Poffins!
-There's no way to change the name of your main character after you start the game. This has bugged me in every single Pokemon game I own; I wish I can change the name of my Colosseum character, especially...
-Two words: Surf speed. Nowadays when I play Emerald, I go "Wheeee!" when I Surf because I'm used to the slow D/P speed.
-If you don't pick Chimchar as a starter, the only fire Pokemon available before you defeat the Elite 4 is Ponyta. X_X
-Geodude appears ALL OVER THE PLACE! It's annoying because it can Selfdestruct, and if I'm training a Normal or Fire-type Pokemon.
-After you defeat Cyrus at the Spear Pillar (he's tough to beat in the first place), you immediately have to battle Dialga/Palkia, and you don't get a chance to heal your Pokemon inbetween. Both times when I did that, I only had one Pokemon able to battle by the time I faced the legendary. Good thing I had some Revives...
-Murkrow/Misdreavus seems harder to catch than Dialga/Palkia does...
-You can't get the Razor Claw (needed to evolve Sneasel) until you beat the Elite 4. It's especially annoying because you can catch Sneasel before the Elite 4, but then it's stuck a Sneasel until after the Elite 4.
-Those stupid boulders in your Secret Base, and the fact that they're so hard to remove.
-You can't migrate Pokemon from GBA games until you beat the Elite 4.
-Before you beat the Elite 4, the only two Pokemon that can learn False Swipe are Kricketot/tune and Sneasel. (Though I admit a False-Swiping Sneasel is useful for capturing Uxie/Mesprit/Azelf because of its immunity to psychic attacks.)
-You can't get the Super Rod until after you beat the Elite 4.
-You can't change the nickname of a traded Pokemon. I wish they would just display the original nickname of the Pokemon in its Summary, and you can change the current nickname however you like. I hate getting unnicknamed Pokemon in trades because of this...
-You can't get the non-letter seals until you get to Sunnyshore City, meaning until you get seven badges and battle Dialga/Palkia.
-You can't display more than one picture of your own Pokemon in the photo booth in Jubilife City. Moreover, why not allow you to display the picture in the Pokemon's Summary?
-You can't deposit a Pokemon in the PC when it has a Ball Capsule on it! I wish you can just keep the capsule on while it's in the PC, so you don't have to apply it again when you take the Pokemon out.
-Your Secret Base appears in the Underground instead of various places in Sinnoh. I liked the concept of secret bases better in R/S/E--even the variety of items available there was better then in my opinion.
-You can't catch Ditto until you beat the Elite 4!!!