This is a pretty good game; I'm actually really surprised that it hasn't gotten more attention. It's complex, but pretty elegantly designed. Graphics are good and it runs smoothly on my system. It's rare to see such a fleshed-out, polished RTS implemented in Flash, so I hope this gets the recognition it deserves.
That said, you lose points for two things. One is that, despite how much work goes into just the RTS basics (a lot, I know) this doesn't add a lot to the genre. You've got economy buildings and factory buildings, you've got towers, you've got ships, bigger ships, and ships that are bigger than that; that's a solid foundation. I've seen a lot less polished games either borrow concepts from other genres (e.g. control of a unit so that it's like a shooter, level up so it's like an RPG, etc. etc.) or come up with cool new stuff of their own, but I feel like I've seen everything in this game before. The other point is that you can't save your game without registering elsewhere. That strikes me as obnoxious. We have the technology to do a local save, so provide that option for the single player campaign. I guess the game was short, but I still didn't want to go through it in one sitting, so I'll probably never get past the level with the colony.
Anyway, tl;dr - good game, add local saves, keep engine, add more variety of units or upgrade paths or something, add more levels. Solid 3.5.