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It's not just that the pokemon models have an absurd number of polygons, but also that you've got dynamic shadows rendered at a way higher resolution than what you'd usually see.
I think they wanted to make battles look as clean as possible but as a result they ended up skimping on lots of other stuff and got something that didn't run particularly well.
I don't want to put too much trust in GF, but now that they've got their pokemon models that they can reuse for many years to come, they can probably put all that time and effort elsewhere instead. XY will probably be treated as the 'transitional generation' in a few years.
