You can get more resources in campaign mode by not finishing off a wave, and thus your mining stations more time to mine. On some levels it's a trade off, HP for resources, but on some like level 4 you have 4 distinct waves and the flier can't damage you as fast as your shield recharges.
"I found str/def/rep to be totally unbeatable." Even the empty genome is pretty much unbeatable at the final levels. The trick is to madly rush to take over all empty cells even if just with a single unit, then if need be use the special cells to your advantage.
Too unbalanced -- the later levels are too easy due to having awesome weapons. And it seems that the antidotes appear randomly in places you can't get, such as two far apart so that you must run past them, or even near your car. Meanwhile, it is trivial to collect them all if you felt like it because the ones you got never show up again.
The formula for points gained for a combo of size n is points = n*(10+n). So a combo of 3 hits would be worth 3*13=39, while a combo of 7 would be 7*17=119, and for 50 would be 50*60=3000. Presumably getting combos in missions increases your fuel, but I don't know whether it follows the same formula. However, in missions you're almost guaranteed to win if you keep your tank as forward as possible, and you won't even get halfway if you keep your tank far back. This badge is going to suck, have fun jumping into the pits people!
How not to make a great game: When loading the level, make the player wait a while before starting but have no way of knowing exactly when. Make each challenge mode stay locked until you complete the whole set of levels again and again. Make the user go to a different website to play skirmish. It would be a very nice game, but it is definitely a downgrade from the original Nano War.
Free advice: get the extra units upgrades. A fully upgraded chargor will give 13% attack power, 5 range, and 17 HP to (nearly) all your units. Note that the achievements screen can give you extra upgrade points.