Well nowadays it's so easy to make a hacked .pkm that is in no way at all different than a "legit" Pokemon, (strictly from a file structure standpoint), they would not be able to check if it's made with pokegen or not. Unless you're dumb/newbie and don't know how to use the programs right.
If they allow importing, we will see Pokemon that are technically "hacked" but they are still the same as if you spent the time raising it. It just pisses off other people that don't use these programs because on Day 1, you can have a pretty good team of 5th gen and below Pokemon.
Most of the time hacked shinies are easily identifiable so hopefully most of those will be stopped if they allow importing at all.
As for me, I'd rather have a fresh start for this generation. I was never one to keep my Pokemon from FR all the way to BW, so I don't care either way. You still own those games, play those.