Hmm, picking the better bot teammates helps to a degree, you just have to do some bloodrites to get some of them. Also, all the characters make thier way into the freepool towards the end of the game, even characters like Xan, Malcolm, Brock etc.
The toughest levels do seem to be the assault levels, Robot factory and Mothership are tough.
As for the final boss (Xan, Malcolm, ClanLord), yes, timing the shields is essential, plus the vials near the super shield are important. And remember, you can drop down from the top of the ship right next to the super shield, and you can dodge jump into the ramp from the bottom level to the super shield as well (the boss does this too).
To beat the boss comfortly, play a defensive game, in other words, stay away from him while blasting him with your shock rifle. If he gets to you, he'll go flak monkey on your ass everytime. Also, try to have some cover nearby incase he pulls out his minigun (the only weapon he can kill you with at long range). Keep playing a defence game till the time runs out.
I beat him 6 to -4 this way (yes, he fell into space all 4 times!).
