We'd like to object. Pokegen does not aid you in creating perfect Pokemon at all. The only reason many 5th gen hacks cannot be detected by either PokeTransporter nor Pokecheck is because the seeding is dependant on the DS's MAC address, thus there are almost limitless options to choose from.
However, once hackers try to touch 4th gen (or god forbid, 3rd gen) hacks or even just Wonder Card Pokemon most of them hit a glass ceiling an amateur is not able to break. These kind of Pokemon have very rigid seeding methods and you only have a handful of legal IV spreads. Not only that, these IV spreads are always tied to a certain PID and nature because they are generated by the same method. Pokecheck will not help you with that (it only automatically sets the gender wheny ou change the PID); even a little slip up and the Pokemon becomes illegal. Technically ...
Pokecheck catches these flunkies just fine most of the time, it even gives a few false positives because it is unable to realize chain-shinies. However, PokeTransporter will still let them through, probably because it doesn't properly check the PID. In our opinion this one is a terrible excuse of a hack check.
We don't mind hacks in general but we still think that people are better off not touching this kind of stuff when they don't know what they are doing. It is kind of annoying when we cannot wholeheartedly trust something we received via online traiding and have to handcheck everything before deciding to keep it.