Very good basic idea. Can be improved in the UI department. Assigning units is too cumbersome. Units data should be available on battefield and upgrade screen. The resource system is a bit strange. If following the objectives and killing minimal enemies you end up with less resources because you have less kills?
Nice game
Has a few weaknesses:
Starting money allows you to buy any store right after buying the cheapest one.
You cannot upgrade or buy a new cash register such that it can cater to all the customers, its a very limiting factor.
If the queue to the cash register becomes long enough, it will stop working all together the rest of the day. All customers will eventually return for their CDs.
Only useful tip in these comments for beating the game on hard level: sell the fighter bay making the ships easier to hit, buy 8 or so fighters on final level to avoid damage
16 level 3 electron towers combined with 2 power amplifiers will complete any level. Thus the power amplifier should be percentage based, not points based. The engineering skill seems to be twice as powerful as any other skill.