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Deadlines, man. They had to make an entirely new game engine on a new system, make a ton of models for said system since X&Y weren't out yet so they couldn't use those, and then near the end almost certainly had to rush it because of the impending release of X&Y in Japan. All in all I'd have to say it turned out pretty well given the circumstances.
Now that they've got the engine, the resources from X&Y, lessons learned from PMD2, it, and the WiiWare, and an entire gen's worth of time to make the next one you can be sure that PMD Gen VI is going to be fucking awesome.