But balancing isn't just about Asset A > Asset B > Asset C. I think the biggest problem is the relation between Time <----> Space <----> Assets, like it is in the "Real-World-Warfare". And that exactly why I think aeros are overpowered. The maps are too small for their speed which leads to an all-time-availability of air assets. Air assets aren't supposed to be all-time-available unless they are choppler-similar like the Hawkmoth. Map sizes are also too small for LongToms, they can cover almost the whole map with fire. The maps could be too big for BAs - but you handled this problem well, by making the BAs not only nimble, but also fast and you gave them the option to spawn at APCs.
I think you're on to something here, but current map size may be as much limitations of the Crysis engine as design choice.
Aero *is* extremely mobile compared to the size of the maps. It's a matter of seconds to retreat for ammo and repairs, which dramatically increases the survivability of the air units - they're always at full health.
Assuming larger maps are possible, I can envision capturable forward bases and mobile repair trucks for mechs. The Mechline can steadily advance with a shorter distance to repair and rearm, but the Aero is still dependent on its fixed bases. As you advance to the enemy base you're further and further for your air cover, while closer and closer to his - this strikes me as a highly natural balancing mechanism over longer rounds.
That aside, I'm not in favor of Mech only servers. The two current Mech only maps are also the two most boring, and I'd go so far as to say Thunder-Rift is broken. On Marshes you can still pull off flank runs, and the LongTom / Raven combo can break up logjams nicely. On Thunder-Rift the LongTom's aren't as useful thanks to the cavern roof, and flanking lights and mediums get funneled into choke points that cut off their mobility. It always ends up as a slug fest over the bridge. In SA mode it just comes down to who managed to win the first few engagements and now has the heavier Mechs.