I think it would add to attack/defense tactics if a new tower attack style was added, similar to the mass ranged attack creeps can use. I was thinking something like a bombard -

tower.bombard(x, y) - Launches a mortar into the air, that lands the following tick. Deals 50% tower damage to the impact site, and 25% to every tile around it. Damage scales opposite to tower.attack with range, so >=20 tiles would be 600 (50%, 300 at impact site, 150 damage to 8 tiles surrounding impact site) and <=5 would be 75 at impact site, ~38 surrounding it.

I like the idea of the root controller, but I'm not a big fan of making no GCL progress from any other room.

What if the "Root Controller" was a structure you built, limited 1 per player, buildable at RCL 8 for 1 million energy. Upgrade points put into a normal controller give half a point to GCL (in addition to upgrading the RCL at a normal amount), and points in the root controller give double.

You could even put in a danger aspect to it - If the root controller structure in a room is destroyed in any manner, you instantly lose claim in that room. That would also act as an impediment to players changing their root controller locations.