One major thing about D/P that annoyed me is Surfing. I could not get over how DAMN SLOW YOU MOVE WHILST SURFING!!! To make matters worse, there was no way of going faster! Finally, to make matters even worse than that, there was none of this stupidness in Generation III - in those games you could Surf at a very good speed. I certainly hope the clown who decided slow surfing was what the people wanted was promptly fired.
Another major issue I have with D/P involves Battle Tower. The amount of Double Team spammers you get when battling NPC characters is infuriating - they may as well say on entry "Oh by the way, bring a Phazer or a Pokemon with a never miss attack, because we're all Double Team spamming cheeseheads over here!" Doesn't make for a good way to test your Pokemon out really, especially for those who play under Evasion Clause since they won't even see Double Team in a proper battle against another player.