You sure? I'm fairly sure, in a raw fight, Bravo would kick Alpha's ass. Alone, Etain is probably the strongest fighter. Then you have the magical aerial support of Kite. Not to mention, Trigger could co-ordinate it all and use sniping tactics/recon to assist in hunting parties. We shouldn't forget the utility of Varos, either.

The side with Amnesia is going to have an advantage regardless due to, of course, Amnesia, but if you assume Etain and Kite are keeping him from using his ability on each other, then you can keep that avoidable. Marquis may copy abilities, but he won't use them nearly as effectively - especially considering Etain is thousands of years old. Trigger, assuming he's fighting from a distance, has a natural advantage to both Amnesia and Marquis whom both have to fight close range. Flo is also primarily close range. If Varos uses wind manipulation to keep them at a distance, the Alpha team basically would have to resort to a firefight and then Trigger is one gunshot away from putting them at a severe disadvantage.

The advantage to Alpha is that they're a significantly better hunting party while Bravo would likely win out an actual versus match. Even still, Alpha team is somewhat supposed to be superior.