Very good work
I like playing turn-based strategy games like this. This one is very well made. I especially like how you can completely reallocate points earned to suit the mission at hand. The music suits the environment well too. That info box at the bottom right is helpful for keeping track of things.
Here are some things I noticed:
I notice a slowdown when you're on the upgrade screen. I have a dual-core AMD Athlon X2 4800+ which should run this flash just fine. I'm not even sure if it's a processor shortfall because when I look at Task Manager it shows only 1 or 2 percent being used for Flash on that screen. This screen marrs an otherwise smooth experience.
I once sent a trooper to a quick death when a horde of aliens came spilling out of a wall. It's difficult to tell which tiles they can come out of. It'd be nice if it were easier to distinguish spawn points although I guess it was just a tactical mistake.
Keyboard shortcuts make this game much easier to play. In the help menu it says that "ZQSD" can be used to scroll the screen. It isn't, not on US keyboards at least. Also having a key for 'Alert state/Normal state' may be useful.
I couldn't tell if reloading uses up an entire clip even if you still have ammo. For example if you had 50 ammo remaining but decided to reload early would those 50 bullets disappear? Would be good to clarify that.
Minor grammar issues. Doesn't affect gameplay though.
A toggle for grid lines would come in handy during the missions. I couldn't tell how wide the halls were sometimes meaning I wasn't sure if my soldiers had line of sight or not. Having the cursor highlight tiles it's positioned over would work too.
I'm just nitpicking but those text boxes in the introduction to each mission should have an arrow or 'click to continue' or something.
All in all however this is a solidly designed fun to play game with a good story. Great work.