You really need to allow replaying previous levels for cash. It's too easy to end up in an endgame death spiral of needing upgrades to survive the crazy ass roads but not getting enough to pay for upgrades because you don't have the proper upgrades in the first place. Easing up on the time limit would also work (maybe gradate the payout, like getting 100% payment for meeting a par time, then reducing the payment by 25% every five or ten seconds over).
Ore needs to bounce off the edges of the map or, perhaps, get automatically collected if it does. Making it unreachable in trees is fine, though, since that gives the player further incentive to deforest the maps.
The rocket towers should either have their projectiles move faster or get a significant damage boost. As is, they're of questionable value compared to the cannon towers, which are hitscan and have a faster rate of fire besides.
If you want the game's rating to go through the roof, add an unlockable rocket launcher. I thought Fable NPCs were the most obnoxious ever. Good lord, was I wrong.
The training minigames are wildly unbalanced with regards to stat gain. Take the climbing set; I can consistently get about ten levels from the second minigame (taking one minute), whereas the third will usually get me fewer than five levels despite having several times the duration. Neither is particularly hard to do, but #2 is simply more efficient. The shortest solution is probably to let the player pick which mingame to play instead of making them sequential.
Instead of making W a (frankly useless) melee attack, how about making it switch between whatever gun you're holding and your melee weapon? That would solve the boss issue (as he really is impossible if you can't find a gun, even with the chainsaw) without completely altering the game. The other possibility is to make melee attacks more powerful (against the boss, if nothing else), but that would probably break the game.
It would be nice if you could deselect upgrades, as in click a few ticks lower on the upgrade line to reduce the effect. As some people have mentioned, upgrading the wings all the way makes the plane too twitchy to effectively maneuver between mines.
Helicopters have some hit detection issues. Basically, whenever they fire at a building from the side, their shots don't hit. This would be less of an issue if they didn't insist on *staying* to the sides, though (seriously, it got to the point where my entire heli fleet was parked off-center, merrily blasting the ground; funny, but a waste of upgrade money).
Noted for a future build. Will add that stat for you to check.