The only suggestion I have is that we are able to purchase a health pack or slightly increase the drop rate/repair amount. It feels as if power upgrades must be used sparingly to "heal."
I don't see the point of having a "time" bar for each character. They're supposed to make it to the exit but unfortunately the heroes ALL run out of time before they can even complete two floors. I understand the point that they're supposed to be doing things quickly but when the heroes can't actually complete anything we're forced to repeat the same floors over and over and over.
If you're having trouble with the last mission quickly expand to the drone tech upgrade with collectors. Build two drones, one at a time, right next to your base and have them target the depression on the left and right side. The center of the depression won't flood towards your base. Once you have the pair of drones attacking continue to expand with collectors until your starting ridges are covered, after that it should be easy.
SAMs shouldn't be needed until after the first spore attack. Two should be enough, four tops.