A Battle Frontier is certainly a good idea, especially since the doing-away of Sig Moves. (That's the one thing expected from Gym Battles...A TM.)
Although, if you wanted to be *really* sneaky and still have TMs, you could have them for moves a Pokémon might not actually learn, but could perform. (Rapidash using E-Quake, Gyrados using Aerial Ace, etc.) To the best of their abilities.
I think that the best way to select the Frontier Brains is through a Tournament. However, there's a drawback to this. People who have been here longer and have evolved/stronger Pokémon would most certainly get all the spots.
This shouldn't be the case. Even the first few gyms were "easy" to beat.
I think that there should be 1-2 Frontier Brains kept open for those who have weaker/nonevolved Pokémon. The 'Newbies' if you will. This would give an even, fair chance to participate. If you wish to apply for a Frontier Brain tournament, then you can choose *which* position you are applying to. Nonevolved/weaker or Evolved/Stronger.
Weak Pokémon could include Babies, weak-stated Pokémon from the games, etc.
Strong Pokémon could include strong-stated Pokémon (Dratini, Larvitar, Beldum, etc.) and no-Evolution Pogies with good movepools/type combos.
Yeah, I want a chance at becoming a Brain myself >.O *twitch twitch*
All in all, its a good idea. If you're confused by my suggestion, please tell me >.< I'll try and put it into a more simple format then.