I would like to see fleet separated from the character areas, and then maybe grant some bonuses for each area that is cleared. This gives people incentive to work on both, because right now you can have a crap fleet and then just "gate" it with crazy strong teams.
Instead of the formation of squad, and then fleet on top, and then squad and squad on the bottom, I think it should be fleet and fleet on top (for the higher divisons, maybe just 1 for the lower), then squad, squad middle, and then squad, squad on the bottom.
This would allow people that prioritized fleet a chance to actually use them.
The bonuses I mentioned could be similar to the bonuses in the TB. If I beat the fleet area, maybe give some form of the airstrike for when i'm fighting the squads. If I can beat the squads, maybe give some form of the ion cannon to assist with the fleet battles.
This would promote equal work on both fronts, and help those that dont have the top end toons or fleet maybe have a small chance of winning - you could even charge banners per ability activation or something. So if a 5 v 5 clear is worth 60 but I used the airstrike, only pay out 55 or something.