I guess that's why new systems exist. The more powerful the system the game is in, the more Pokemon they can fit in. The problem is that the graphics and gameplay part may not change much because of this. In other words, I think the new looks of X and Y will be definitive and will be repeated in all future main games, so when a new Gen begins, they don't need to worry much about the other aspects of the game and focus on the new Pokemon added.
However, we've actually saw this limitation you talk about in the new Mystery Dungeon game.