Battles:

Core parts to battles:
Moves (4 moves from one pokemon 4 moves from another)
Damage 
  Effectiveness (ie: Its super effective x2 damage)
  Moves (Base Attack)
6v6 (You can switch out your Pokemon if one of them faints. The opponet will switch out the next one in line if that faints)
Rewards (Money, Exp, Trainer Exp)
  When you gain EXP from battles, your Pokemon must level up (Formula is level cubed)
When you leave the battle page, that your battle thing is deleted (figg.php is include in every page, and I think thats what its used for)
You must fight the party of the trainer (The 6 Pokemon that appear in their profile) (If they have less than 6 only battles that number)
Macro Dection (So people won't use iMacros and things)
Restart Battle (So you can keep battling and restarting, even if you lose all your pokemon)
Clans
  Clan Wars
    If the clan is in a war with that clan, they gain extra clan exp
  Clan Exp
    Clan Exp used to level up, which gets you Clan Points.
    Clan Points used to buy things like a Reward Bouns (1%, 2% ect) and a Damage Bouns (1%, 2% ect.)

Extra things (Would be nice but they are unnessicary):
Items (ie: exp. share, amulet coin)
Status (ie: Asleep, Poisoned)
Special Moves (ie: Hyperbeam has to wait a turn before it attacks)

Setup:
Try to have the stats at the top (The HP and picture and stuff)
There needs to be a place to pick moves to use
There needs to be a status box (Where things like, 'you did 15 damage' and 'You got 1,000 expirence points' go)
There needs to be a capatcha (When you do a certain amount of battles, a picture comes up and you have to enter the code in, you've seen it before)

(The '<br>'s just mean to put the thing on a differnt part, like not next to each other) 
Pokemon name - Level <br>
Pokemon Picture <br>
HP - Current HP/Max HP <br>
HP Bar (A bar that shows how much HP you have left) <br>

Formulas:
Exp to get to the next level = Level cubed
Exp = Level * Base HP * .70 + ((Level * Base HP * .70) * Clan Reward %)
Clan Exp = 1 + Clan Exp Bouns (* 2 if the person you are fighting is in a clan war with you)
Trainer Expirence is just the expirence you get. The point of it is like a total of the exp you have trained yourself.
Money = Level * 5 + ((Level * 5) * Clan Reward %)
Damage = (((((2 * Level / 5 + 2) * AttackStat * MovePower / DefenseStat) / 50) + 2) * STAB * Weakness/Resistance * RandomNumber / 100) * Clan Damage%
         Check out http://www.serebii.net/games/damage.shtml for more information
		 Clan Damage is something thats for TPK only, its an upgrade you can get from clans