^For my Mudfishy self, that was Zapdos...Aggh, how annoying it was...
The main flaw of the PMD games was the lack of things to do after the story.
Post game in the regular pokemon games, you have the battle frontier, which is just as hard, if not harder, than defeating the elite 4, giving you a goal to accomplish after the storyline is done. In addition, you can also play against your friends with it, battling or trading. And if you don't feel like doing the BF, there's always something else to occupy your time..Contests in R/S/E/D/P/P, Pokeathalon in HG/SS, and Musicals in B/W. There was just physically more you could do with the game even after the main story line was complete, whereas in MD, after you finished the story line, you're more or less left with recruiting rare pokemon, and completing repetitive missions. You can't hook up with your friends, other than rescuing them if they faint in a dungeon, and even then you're playing separately from each other, even if the two of you might be in the same room. In addition, it becomes a long and boring task if you want to train new pokemon, because they can't survive a hit from a pokemon in strong level dungeons, and without any EXP bonus item, level up incredibly slow in weak dunegons. And even if you do train up these new pokemon, there's nothing to do with them afterwards (Can't trade or battle friends)...Except keep completing the same missions.
So, yeah. The story was novel and intriguing, and the game play was enjoyable, but there just wasn't anything to do after you completed the storyline that made it worth playing more.