Okay... make way for detailed post....
The fact that only challengers can sub pokemon will screw us all over and make us easy bait, especially if we're using onlyone specific type. I suggest you make yourself at home here first and learn how we battle. It's quite different than stuff you see on TV or any other weird battle schematic.
In the Pokecommunity battle forums, we have an standard set of rules, which aren't set in stone, but almost everyone goes by these.
From Shiny Umbreon's "Battle Me" Thread. I altered it a bit.
Rules
Pokemon Carrying Limit.
This is simple as said... right? though you don't have to battle with 6 pokecom each, it is pretty much what everyone does. You are free to change this rule, since this is your thread.
Specify Whether you want battle caps to be at Level 50, Level 100, or No Restrictions "Free" cap.
Also does not really have to be explained... allow battles to be either lvl 50, 100, or just no restrictions. For example, if you allow battles to be at lvl 50 or 100, each player's pokemon will all be either lvl 50 or lvl 100. This is basically used so we have fair game and don't end up with a lvl100 Dragonite fighting a lvl 40 Mr. Mime. Hmm, I wonder who would win...
No Ubers
This is imperative and strongly enforced here. No Ubers means you are not allowed to use said pokemon for the purpose of them being too strong against normal pokemon. Ubers are usually categorized by their imbalanced stats, high IV/EV value, making them obviously more difficult to defeat. Again, all these rules are so that we have fair game.
No Hacks
Another well enforced rule. This means NO HACKED POKEMON to be used in battle! If you have a Spiritomb with Wonder Guard Ability, which only Shedinja should have, isn't it obviously hacked? These are not allowed or wanted anywhere, and if you feel proud winning with these Pokemon, I suggest you not to enter WiFi Battling for any reason whatsoever. Also, obvious moves that a Pokemon should not normally learn, say, a Pikachu using Flamethrower (Blazichu! xD) then it is also hacked. Some people try to hide altered stat Pokemon by using a program called Pokesav, but that is also identifiable, because it will have spaces at the end of it's name. If it has spaces, and it is suspiciously too powerful, then you can take a guess to know that is has be Pokesav'd.
Normal Pokemon: CHARMANDER used ember!
Pokesav'd Pokemon: CHARMANDER used ember!
OHKO Clause
Nobody likes a pokemon that can take you out in one blow no matter what the situation. OHKO stands for One Hit Knock Out. This clause states that pokemon may not use moves such as Guillotine, Sheer Cold or Horn Drill. If a move like Lock-On is used, then it is certainly 100% bound to hit. This ruins the fight in the opponent and he will most likely lose. Make sure you enforce this, along with other clauses that you feel is necessary or else no one will battle here.
Evasion Clause
Evasion Clause states that pokemon may not use moves like Double Team and Minimize. If used to the max, that pokemon will never be strikable, thus causing it to be near invincible. This is also a good rule to include in your thread.
Sleep Clause
This clause is different from the others. This states that you are not allowed to put your opponent's entire team to sleep, better yet, you are only allowed to use a sleep-inducing move on no more than one of your opponent's Pokemon. However, if your opponent used the move Rest, then that pokemon has not been put to sleep by you. If a pokemon used Rest, you are allowed to use a sleep move on another one of his pokemon.
Hax Item Clause
This means certain items may not be used because they alter luck-related moves, like critical-hit assisting moves. I.E.: Razor Claw, Scope Lens.
This isn't really that important, but with this clause in effect, it is ever more equalized and battling will be more fair.
Whew... Now go to your first post and specify! :D