As randomspot555 put very well, wi-fi and shoddy are very different enviroments. I don't know how much you know about programming or whether you have looked at shoddy's source but looking at it and learning about how it has been created makes me sad. Sure the reason's for doing it the way they did are legitimate. But people taking as fact that rules should be based on shoddy's result is what makes it so bad.
However, for Shoddy Battle 2 Colin is using research from the game for many things where it previously was not used, meaning it will be closer to the real thing as far as battles go. Of course, the environment will still be different for the things already stated.
Also like randomspot555, said, we will be assuming use legit pokemon. The apparent cheat detection that takes place when trying to summit a battle with the VS Recorder seems like it will help sift out cheaters.
The people making shoddy do not have complete knowledge of the battle mechanics so you can't expect them to be the same. If you claim they are and you want to defend their results then you'll have to provide proof that they are the same.
There is a glitch in the function that generated the pkm that will go into your party/box from the roamer information. Before its copied, the data is fine, but in the process, the IVs are not copied correctly so you end up being able to get up to 31 in HP and 7 in Atk.
Well, its correct if its only applied to battles taking place using Shoddy.
For the ones from Colosseum, they don't suffer the same problem.