I really like the concept of this game a lot, but the execution lacks here and there. My 2 cents:
Recon Mode is useless. Mainly because Overkill does not work in recon mode, the bonusses it provides will never be active in a normal run in the waves where it actually matters. Advice: instead of the Recon bonus going down with each kill, let it go up each second, stopping at the highest kill count from recon mode.
The effect of higher levelled troops is almost uselessly meager. In order to even double your damage, you'd need Rank 2 troops counting half of your normal troops, which you will likely not reach for ages. Considering that the average HP multiplier between waves is 10, every EXP point spent on troops is wasted considering their "impact". Advice: greatly buff either their damage multiplier per rank or their production, or both.
Energy upgrades don't carry over excess energy when they level up. That simply doesn't feel right.
Possible bugs:
The "increase energy cap by +10" prestige upgrade doesn't do anything.
Tactics are only effective for 4 seconds instead of 5, as described.
Thank you very much for making this game. You've got a good concept that needs some tuning here and there. Looking forward to what you're going to do with this game :)
PS: an export/import function would be dope, in case I decide to download the game so I don't have to start over.