The CMC Pokèmon League

I honestly hate Shoddy, but I would also suggest that it should be considered as an Alternative for this specific endeavor. Not only would it make it highly accessible to the forum in it's entirety, it is also a great time saver for anyone interested in this thread. Training Pokemon is very time consuming which is a huge reason as to why Shoddy is so popular. The way it's set up is that you can assign-- not stats-- but Effort Points and IVs to Pokemon as you like. These change the stats, but the changes are legal, unless you go beyond legal bounds; Shoddy notifies you if you do though. Aside from that, there really is no way to cheat, and this form of cheating is an issue with Cart Battling anyway and more difficult to prove. In Shoddy you can sit in on battles and see if people do in fact Cheat, whereas DS Battles it would be one voice vs another. This goes for Clauses as well, you can set Shoddy to have the Clauses you have stated above (Freeze Clause I'm unsure of, but definitely the rest.) Anyway, avoiding a rant...

Smogon is really not a bad way to go.
I'm sure the only reason Nintendo hasn't set up something like it is because they want people Buying the Game. Are you working for Nintendo? o.O;;

And your concern with Hacked Pokemon, and Illegitimacy:
People can easily avoid being caught on WiFi, it's a bit harder on Smogon, so if this is truly a concern, you should go with Smogon.