I am currently stuck in the second part of the final mission: The Endboss already came down to the ground, wielding shield and gun and there are LOADS of enemys. In the beginning Lannis says to split up and take them out on two routes, but I just stuck together as a team, connected the floating islands to the main island and let the enemies come to the starting point. All my characters are in full cover, #13 is beaming around the crates and dispensing the healthpacks he finds. I always get overrun. What do you guys do? Stick 13 in the prototype tank and have him block the path? The problem is that the enemy aims much better, even than all my level 10 aiming characters. Grenades do nothing anymore. Anybody want to share some tactics?
I usually go up to the two forward islands, grenade the melee guys as they come up and have Thirteen tank the boss while my snipers stay way behind and take potshots at him. The ranged guys stay so far back they're no threat at all and if you beefed up Thirteen with enough health packs the boss won't be able to two-shot him.
Spoiler hint: If you focus your fire on the endboss and kill him, everyone else will day afterwards. You do not have to kill all the other enemies. But then, some of them may be in your way. Hope this helps to finish him off.
I know I might be a bit late, but since I've had problems with the last boss myself, I decided I'll spread the good news. Just a friendly warning - this method may prove to be very unfulfilling. So. Use steady shot to snipe the Big Violet Bad across the map. You'll notice that you've actually took a good chunk of his health away. Order all the remaining characters to take potshots at the boss. Rinse. Repeat. None of the enemies will move or try to respond with fire. At worst the boss will occasionally go into retaliate mode but don't let that stop you. Sooner or later you will bring him down. Congratulations! Now go and make some nice mods.