Have you thought about making the infill of new tiles come from a different direction?
With infill happening at the top and blocks falling down, towers end up being 'thicker' at the bottom than at the top. This makes towers that shoot vertically or diagonally 'feel' more powerful than towers that shoot forwards (and I think the top scores would support this - everyone uses wood, and often dark towers and water).
If infill came from the 'front' and everything 'fell' towards the back, then towers wouldn't be rearranged vertically except by direct player action, and choosing which row to place towers on would become more predictable and strategic. I suspect it would make horizontally shooting towers more balanced against vertically shooting towers as well.
I suggest infill from the front rather than the back, as you generally want your most powerful towers in the back, and giving the player what they want is often a good idea. That said, if the enemies removed more than just walls, pushing towers forwards and into the line of fire does become interesting... but destroying towers creates a significant positive feedback loop where if a player starts doing badly they will have trouble recovering.