The story of DDD is far too convoluted for anyone to reasonably follow without extensively researching and discussing the series online. This isn't helped by how much the game doesn't explain and how frequently it seemingly contradicts itself. I'm a huge fan of the KH series, and have never considered it all that complicated, but DDD definitely changed that. I also love time travel stories, but this one was executed poorly, with few rules clearly established and several seeming rule-breaks in that very game. Further, the game is a fountain of retcons. Ansem SoD and Apprentice Xehanort's motivations make little sense now. Retcons are fine, and I'm no slave to past canon if a change is needed to tell a good story, but this game's story is sloppy and confused, and it sacrifices some of the most powerful material in the rest of the series to build up some poorly conceived master-plan.
As far as gameplay, I enjoyed it, but it was a step back from BbS (like most everything since BbS). The Flowmotion system is very fun and exciting, but it was balanced poorly and mars the series' move toward more strategic combat. It also wrecks DDD's only feeble attempts at platforming. Similarly, the lack of command fusion was disappointing, especially after Re:coded's very clever system. Spirits were fun as companions, but linking commands to them was a bad idea. I mostly kept and trained the same Spirits the whole game (which I thought was the point of having cute, cuddly companions), so I never obtained a solid library of commands. The spirit links were very cool, though. I especially enjoyed utilizing Sora's links. I'm pretty neutral on the Drop system. I never really used the Drop bonuses, and dropping during a boss fight was stupid, but the system generally functioned well.
On a more positive note, I thoroughly enjoyed the difficulty of the game, and the visuals were fantastic. The music was also (in my opinion) equal to the best Yoko Shimomura has yet produced. The minigames and sidequests were also better than average for the series as well.
tl;dr: The story was awful but the rest was decent