Air / Anti-Air is a problem that has plagued TD for a long time. It serves no purpose, save to add an unnecessary layer of complication to the game. You invest resources into dealing with an enemy that can only be killed one specific way, and if you haven’t by then, you’re boned.
But what if there wasn’t an enemy that ignored the level and went straight for you, what if there was an enemy that modified the level to forge a quicker path to you? In maze-based TD games you construct the path that the enemy walks down. In non-maze TD games, the opposite of that would be an enemy that constructed the path for itself and it’s allies.
For a basic example, we have this:
Cracked Rocks and Wild Growth. Cracked Rocks would be certain places where you couldn’t place your defenders, places that are one tile thick. Something to be ignored, until the Speedy Bomber spawns. The Speedy Bomber rushes from it’s spawnpoint and makes a mad dash for the first accessible Cracked Rock, not unlike the Torchbearer Uruk-Hai from The Two Towers. If it reaches this rock, it immediately detonates, blowing itself and the rock up. Enemies that have progressed past this rock continue on the normal path, but enemies behind it will now have their pathfinding adjusted the newer, quicker route to your Macguffin.
Wild Growth would be bushes, thick vines, trees, anything else difficult to pass through. A slow, tanky enemy with a massive blade would fit for dealing with these, like the Cultist Revenent. These would be several tiles thick, requiring the unit take it’s time slashing through several tiles worth of blockage to carve a quicker path through the level to your Macguffin. If all tiles with growth on them are sliced through by the enemy, as per above all enemies before that point would have their pathfinding adjusted.
You could even adjust this to include Crystals, by making them very powerful aids in defeating a cluster of powerful enemies, but by zapping it you clear the tile it was on and make the rest of the level potentially more difficult for yourself. A desperation move to try and survive to the end.
I can’t think of any other TD game that has had battlefield destruction like this, but it seems like it could be a lot of fun. 
Thoughts?