1. Base EXP debacle:
Not only the current Base EXP list is based on the stats of Gen V, which have been recently changed, it also contain a few major errors, for Clawitzer, Aurorus, Cascoon and Dustox. The next generation should update the Base EXPs to fix these errors, and presumably to fix other EXP distributions.
Even ignoring the fact that contest stats remain part of the Pokemon file system, we have the issue of the contest-only berries, which are still relevant for Natural Gift. As the next generation will likely have Contests as part of D/P remakes, we need to watch out how contest berries and contest stats will be handled.
3.Hidden Power debacle:
Currently, Hidden Power Fairy, nor Hidden Power Normal exists. As Fairy-type is a new type, this is kind of an issue.
4. Moveset errors:
As OR/AS had a pretty rushed release, several movesets were basically defaced. These movesets must be brought back in to shape, as their current situation is too chaotic.