I found that my troops had much better survival rates if I commanded them because the AI will keep them in a shootout until they explode.
I equip every bot with one reparier, then just control a pack of 9. When one of them starts to near death I send him into the back of the clump, meanwhile everyone is healing him while firing their missles. If I'm fighting a huge horde of enemies I'll just keep retreating my guys after they fire a salvo, because while rolling backwards in retreat they heal, but they don't get shot at. Also, when persuing, the enemy AI tends to go single file, so your retreat essentially lets you face the enemy 1on9.
I keep a group of 9 guys at the two or three checkpoints each map has, and am always using one to hit and run on enemy groups and bases. Really the only problem is when one group is engaged on one side of the map while I'm actively controlling the other group. Considering the odds you face in later missions, your groups of 9 will get ganked if you're not watching over them and making them retreat when wounded.
Missle launchers are the most cost effective armament. I use it almost exclusively except when I start getting a lot of plasma, then I start replacing them with plasma guns. I virtually always use the dynamo headset, and try to include mortars as well, however these are the last priority. The only REAL priority is that every tank use the quad setup so as to have the most firepower available. And once I've essentially got the match won I tend to make sure I've got anti-grav on all my robots. The unit limits are low enough (plus you can only control 9 guys at a time IIRC) that you'll want to be producing the highest quality robots you can afford most of the time. They last longer, and with the way I play casualties are generall low.
That said, I had to play one map like 4 times until I won because one depot was in a pincer between two enemies, and it would always get destroyed. It took me a while to figure out what the enemy would do prior to attacking so I could pull back and then let them fight each other while I watched. Then I'd move in, kill the winner, and recap the base until I had to abandon it again.
Screw bases. The only thing that is really important in the RTS missions is that you have zero casualties, and that's easy to do if you control the units in RTS mode, and always fight on the defensive. Trigger the enemy, then run back to where the rest of the group is waiting in a semi-circle. They all fire their missles at once and destroy the first one or two mechs instantly. Then if it gets too hot, retreat. Easy peasy.
Oh, also, the only real threat to this strategy comes from suiciding mechs, which usually neccesitate switching to the other headset for a while, until your forces are mixed and therefore can withstand and heal when you do get bombed.
