To make gems more valuable, I think you need something that requires a lot of each type. I suggest adding an upgrade or option that lets you spend 10/100/1000/... of a gem to get better chances at +1/+2/+3/... picks. Additionally, you could add another digit to the chances and make it so that gems can't be combined across colors. With some rebalancing of the drop rates, that should make the higher level gems much more valuable.
There are a few issues that become more and more apparent as you progress. You can jump, but often not high enough to clear an entire set of obstacles, but while you're in the air, your cannon tends not to aim at the ground, so you can't clear the obstacles out of the way either. That means that it's often best to ignore the jump button entirely, but then your cannon doesn't reload fast enough (even with the reloader) to get everything out of the way. It doesn't help that on steep hills it also has trouble hitting the things right in front of you or that the ballista wastes its time shooting at armored guys it can't damage. The stuff raining down on you doing unavoidable damage just makes things even worse.
In the final stage, I got to just past the last gate time after time, no matter which way I played and even after several upgrades. That leads me to feel like skill doesn't matter much in this game and you're really just grinding for the final few upgrades to get to the next level.
The unlock schedule, limited resources, low sale price, swarms of enemies and restricted building space altogether make this a very linear game with no replay value. You can't, for example, make a small powerful ship with any chance of survival. In fact, it seems likely that everyone's ships will end up looking pretty much identical throughout the entire game.
Three bugs I noticed:
1) If there are too many objects on screen, bullets start disappearing. I assume you're using a bullet pool? If so, it's too small for the endgame.
2) The odd numbered explosions always face right. They should flip either based on the ship direction or randomly. (Ok, not exactly a bug.)
3) The special waves of normal ships (horizontal, cross, etc.) have a fixed explosion multiplier like the special ships, but they reset the values of the exploded bullets too unlike the special ships.
Since all the elevators are one-per-shaft, don't make elevators that go all the way up. Make two shafts, side-by-side, one that goes from ground to about 1/3 up then skips a floor before going up the rest of the way (in a new shaft), then another that goes up 2/3 of the way before doing the same. Then the guests that aren't trying to go from ground to the top won't take up the full height elevators and complain about the waits.
Of course, it'd be nice to be able to put multiple elevators in one shaft.
Guns are almost useless. An attack that costs resources should be better than an attack that doesn't, but wasting 10 bullets on a 60% chance to hit each enemy (just one example) is definitely worse than just whacking them with your sword.
It'd probably be more fun if it were a little more forgiving when deciding what's touching what. Also, the scoring formula (40n + n*(n-1)/2) means big combos aren't worth that much more than just clicking each piece, which is a bit odd for this type of game.