Wow, this is getting vicious. You guys really should put this into PMs if you're going to mention the actual Pokemon, or anything you don't want public.
Sorry, but even if you were battling for 3+ hours, you can't decide who was winning with 6 vs 6, unless we actually saw the battle and can prove that what both of you are saying is true. It's possible one of you is lying, but most likely not. You just have different perspectives of how well you were doing at the time.
Make sure you contact Hauntershadow about this if you don't do a rematch. Simply, change teams and battle. If you can't change teams, just get a team, whether it be the old one, and battle! If you really can't sort it out, then get haunter involved. You guys shouldn't be so heated about POKEMON.
3 vs 3 won't help, it's just not 6vs6, and it's too different with just a team of 3.