Yes, that may be the case. Everything I've seen from Gamefreak and how they do things tells me that it took them a very long time and a lot of effort to figure out how to move the franchise to 3D (both internally at their company and in the games themselves). Imagine how much effort it took just to make those 3D models - it's no wonder this gen had the least amount of new Pokemon. Not to mention coordinating a worldwide release and getting all the translators from all the countries on board (I think that was handled by Nintendo, but still, their company undoubtedly went through a lot of changes in this transition). So I think they just barelyyy got on their feet with XY. Now that the template is done (the boilerplate), they should be able to work on story and other improvements next.