I think leaving off EXs is sometimes intentional. EXs are for the most part underpowered, and realistically many single-prized Pokémon are now superior to EXs. I think it's fine to leave it how it is - but only if you are careful to remove the dangerous cards (like Milotic) *going forward*. Personally, I dislike Expanded, and in part dislike it because it's *too big*. Smaller expanded would fix some of these issues, and at that point it might make more sense to do what you say and make it generic. But as it stands now, I think it's intentional that it's not generic.