Been a while (prepping to start a new game now that GoG has Reboot), but if I recall correctly, here is how to make most of the RTS missions trivial:
Hover legs, as many rocket launchers as you can carry, mortar, and the head that extends range. Build a few of these, and at least one that is just a hover with 4 repair arms.
Never have the AI fight for you. Just keep a pool of troops, and then manually control one of them. Fire at the enemy from maximum range (you will almost assuredly have more range than them), and you will slowly but surely whittle them away. If your guy gets destroyed, manual control one of the others. If the others get attacked, they can usually hold their own (because of the range).
Obviously you can still lose (especially the 3-ways where the AI might swarm the other AI and have an entire map against you), but this gives you a VERY good chance.
Beyond that: For your first few games, be a law abiding citizen. You don't want to piss off the military. Do quests with little to no combat (so fedex quests), and do trading with the galaxy search (or whatever it is called) to buy low and sell high. After you amass some cash and upgrade yourself a bit, do a few bounty missions to get used to combat (usually it will just be a one-on-one fight, possibly with support for you if the target is a criminal). After you have confidence and a good ship, start joining in the pushes against the Dominators.
Also, it is smart to start with the missile launcher as one of your free upgrades. It fires seeking missiles with a good damage for starting out, and you can usually pay for more ammo with one or two trade runs (or just selling loot).
Post edited June 07, 2012 by Gundato