I think the problem with the sudden cost issues revolves around the black crawly things that show up around level 3. They give something like $1000 each, which is WAY too much for the costs of everything else, the difficulty inherent in killing them, and the numbers in which they show up. It's like there was a typo there, you added an extra zero or something, thus making them into ridiculous cash cows. Fix that, and it'd go a long way towards fixing the rest.
No, this is most emphatically NOT the most exciting helicopter combat action game ever that makes you fly and fight over desert. Desert Strike, for the SNES, was far more exciting. This is just kinda meh; and is in fact far more cumbersome and boring then the average flash game. Try again.
Earth mastery seems really strong, since it affects poison and cure, thus allowing you to pursue a long-term strategy with little trouble. Water mastery, on the other hand, seems really weak, since it has no associated spell. Maybe move cure to water?
Controls need work, as mentioned. There's also some kind of glitch where it crashes at the 'submit score' screen (the flash app, not my computer), and refuses to accept any sort of input... not sure what that's about; got that one on my third playthrough. Overall, not bad, but needs a bit of tuning. 4/5
If your attack rate is limited only by your clicking speed, something is wrong. Autoclick FTW. To fix this, remove the ability to shoot as often as you click and make firing rate upgradeable.
The tunnels seemed pretty useless... you can't do enough damage that way to put more then a dint in the computer's health, which it can fix almost before you can have another out. The only real way to attack is with the highest-tier unit.