I think some of what was actually done in Diamond and Pearl worked to rectify some of the "meaningless" Pokemon, though they did add a few more. Tangela, Electabuzz, Magmar, and others received necessary evolution upgrades in an attempt to make the Pokemon that are there more relevant, and I certainly don't see anything wrong with adding in more Pokemon when the ones they add improve upon what's already there.
I don't think 3D animated battles are as good of an idea, though. In all the 3D games I've played, I've really not seen anything all that impressive. Most often, it's a video of a Pokemon doing a stock animation toward an invisible wall.
This said, I wouldn't be opposed to an alternative line very much like what you described. Pokemon as a battling/adventure/collection-based RPG works pretty well, but I'm all for a game with more emphasis on individualizing Pokemon, and wouldn't mind seriously reduced numbers if time and effort was put into animation and control of each Pokemon.
