Amazing!
This is pretty much the best thing that's happened to flash RTSes, ever. This is a full fledged RTS, no bones about it. But no, it's not Starcraft; micromanaging unit actions is not even possible, much less a focus of the game. You instead focus on the strategy of the battle rather than the tactics.
The hallmark is a good game is one that keeps you coming back despite its flaws. It is a shame that the average Newgrounder has too little tolerance for an actual strategic dillema.
Defensive buildings are really, really good. Probably too good from a game design point of view, but for people struggling with the game, I suggest using a combination of defensive buildings and an excess of money generating buildings before worrying about going for the kill.
If you're into actual thinking, try out the WBAIC scripts. It essentially means that this is an ONLINE flash RTS, though all your decisions are made before the battle actually starts. Go to the forums on the webpage for this game; my WBAICs are there. Let's fight!
True, the game design has obvious balancing issues (hmm, should I make a ninja that does 1 dmg if it gets in range to shoot, or the longer range splash damage grenade dude?). The AI is not as bad as people seem to think it is; you just need to command your units properly to get them to do approximately what you want. No, you can't micromanage their motions, but let's face it: you can't micromanage individual troop movement in a real war, either. And your opponent has the same issues you do, so it is fair.
Animation and general production value is obviously top notch. I would prefer more control over the soundtrack, but that's a nitpick.
Please don't abandon this project. With a few tweaks, the rough edges that keep some people too frustrated to play can be smoothed, and the in depth WBAICs can be extended just a bit to both make the online part of the game a truly amazing feat and to make the single player battles more in depth.