I used PokeGen for a long time on my SS, W, and B2 and traded PokeGen'd Pokemon to other users on this site.
It is ok to use.
Just a tip: Do not let the Pokemon go straight to your party. Always have 6 Pokemon in your party before getting your PokeGen'd Pokemon so it goes straight to your PC. Once, a Pokemon went to my party and it had no moves. But, I just put it in the PC and it was fixed.
Source: Plenty of Experience