All of it. There was literally nothing good about these games asides from the visual upgrade...and improved aesthetics should never come at the cost of actual game content. Which was woefully lacking in these titles.
I could make all the same complaints of these games that I could make of Gen V and VI. Style over substance approach, lack of player focus in favour of under-developed and thoroughly unlikeable NPCs, unbalanced gameplay mechanics (in this case, Gen V's EXP growth rate making an unwelcome comeback), lackluster designs of new Pokemon, diminished length of the main game and little to no post-game content, washed-out polygonal models, unnecessary removal of certain features, severely lacking character customisation options, terrible music...I could go on. That's just the tip of the iceberg.
I've come to expect all of this from Pokemon at this point. It just never gets any better. It just slowly slides further and further into mediocrity. Looking back, it was Gen VI all over again. Which was Gen V all over again. I was never hyped, but I WAS moderately interested. Looks like even that is too much for this franchise these days.