There are two meanings to top-down AFAIK, GTA 2 style, and Zelda/RPG styles. I think you're going for GTA 2 style.
I agree, its really confusing. You may want to add more shadowing to the one on the left. At first, I thought the one on the right was a side view because of the bottom (thrusters?). There is not enough shadowing on this (the right one) as well.
You should think about the type of genre this tower defense game will fall under. So far it seems like the futuristic genre. Try adding things that glow, and very intricate circuitry.