1) Not lack of pokemon choices, but the SAME pokemon pretty much everywhere you go.
2) Battle Graphics. I loved how G/S/C made the battle real dramatic through the black/white/invert colored screen. Now there's all these fancy backgrounds with nearly every attack. The attack that I love in the game is CONFUSION! 'cuz it turns the screen black, it's fast, but impacting.
3) Rivals... 'nuff said
4) All the legendaries are either part psychic or part dragon. That's a wrong on many levels (Heatran and Regigigas besides)
5) Easy-ness and length. The story wasn't very in-depth, and after you beat the elite four it was hard to train, everything became simple, and there just wasn't enough replay value to it.
Lastly, 6) Pokeradar is hard to use. I barely ever get to play the DS, and the Pokeradar was way to much of a problem. I got to 40 chain of eevee, but after a couple of tries I didn't notice my repel went away... until I took one step. As I was pressing the left button I'm like, NO! I NEED A MAX REPEL! and in that ONE STEP I found a roselia. Wasted an hour of my weekend.
Diamond/Pearl is a great game, an excellent game... but there's a lot to improve in 5th generation.
The snow. Agh! You can go on water. Abover air. Under water. But they don't let you stay on snow. Looks pretty but, Agh!
I hate the mud aswell.
It's a swamp. They should give you a paddle boat or let you surf or something
everything is annoying abt the game but we tolerate it because we love pokemon.
But for me I would say the general slowness of the game, I think i must have mashed my A button a million times just to see the opponent's pkmn hurt themselves due to confusion when my pkmn confuses it. Oh and a lack of a proper training area
A very annoying thing is, not only in D/P but i noticed it a lot in D/P that if you have a Pokemon that learns mostl Sp.Attack moves it will have it's Attack stats like double it's Sp.Attack stats! Even worse if the nature is Impish! (just an example but yeah you get it)