AT LAST! A fellow Free Radical! I've been eagerly awaiting another mission that lets the player control the FR's.
Even without that perk, though, I enjoyed this mission! A few comments...

You have a lot of open space in this mission, and I like that. Ordinarily, I'm a big fan of lots of scenery; a good-looking map makes for an interesting mission. Every now and then, though, my eyes need a break from trying to make out every rocket trooper hiding beneath another group of trees. Your mission provides exactly that: a good, clean map that lets me focus on the task at hand.

Since this is a rescue mission, where you are essentially asked to go into Omni territory and and take over several HQ's to free the leader of the Free Radicals, I think that the Omni forces not attacking your base is entirely appropriate. After all, what reason would they have to be on the offensive if they're safely within their own territory? The player is the invader, and thus on the offensive. The only thing I would suggest in regards to Omni being more aggressive are regular Omni patrols of the galaxite fields.

Bearing that in mind, I was a little puzzled to see that I started the game at an already established base. Now I'm a little predjudiced, here, as I like to lay out my own base. Start me with a few troops and a Dominion, and I'm happy! Not everyone may feel that way, though, so I'll stop just short of suggesting that you change anything - the level plays great either way.
All things considered, it's a great level! I'm looking forward to your next.