I will never understand why Game Freak didnt call in back up for this game. They really should have. Even if it still turned out that not every Pokemon could come back at least it would have decreased the work load on what is a relatively small studio in Game Freak. I hope this game teaches them a lesson to reach out more. They don't have to do it all alone.
I dunno, I feel like they don't reach out because they may think, "if it ain't broke, don't fix it," and the determining factor of it being broken or not is how well it sells--and Pokemon will sell well regardless of the decisions they make (unless they made a really bad one, of course). They may be wary of changing up their business practices and risk being less profitable. It's why I understand the reasoning, even if I fundamentally disagree with them.
I feel like they should have continued adding Pokemon through updates, and in the next game make sure there's little overlap between the returning Pokemon so that they can keep adding returning mons with the new animations, until over time every Pokemon becomes available. But that all depends on how many return in this one--if it's 500, then that could certainly be done. If it's 200 or so, then probably not.
I just personally think it was avoidable--they already future proofed them, so they should have stuck with that, rather than doing new animations, because, to someone like me, it doesn't look that much better and isn't worth it given what they had to cut back. They knew it wouldn't go over well, and I truly believe they're genuine when they say it was a hard decision for them to make--but they knew most people will buy it anyways and I believe that's why they ultimately decided to go through with it.