Clicking on towers to collect gets old really fast. There should be a "next wave" button in addition to the speed button. There should be an indicator of damage to the primary reactor. Towers should show range circles before they are placed.
Overall, decent game. The achievements are a nice touch and the upgrades are handled well.
Unit selection is either buggy or just poorly designed. The chat story might be good, but presenting it One. Line. At. A. Time. is just irritating. Minimap should show which areas have been explored. Overall, a decent start but it has a long way to go before it is good.
Well done. Lots of upgrades that give progressive, noticeable improvements. Here are a few suggestions to make it even better:
Maneuverability upgrades.
A stats screen showing things like DPS, energy consumed/recovered per second, etc. This addition would allow for better informed weapon design decisions.
The ability to load a previous design into the weapon creator. Currently only the most recent design shows up in the creator, which makes keeping more than one type of weapon upgraded problematic.
When I heard the disembodied voice advocating murder, I figured it was Satan tempting Nephi to sin. I expected to choose whether or not to kill the defenseless man.
There is retro style and there is just making an ugly game. You have achieved the latter. The metroid-style unlocking of new areas is a decent idea, but it needs a lot more polish.