This is more of a tip than a solution. For the final level the hordes of enemies leading up to the boss fight against Mr. Sinister. For the big belly flopping clones use shotguns you should kill them pretty easy. Then you will have to face a variety of enemies, for the melee foes you want to switch to the plasma rifle and use
when it shows above their head to counter them you should kill them fairly easy and you do not waste ammo.
Now you want to run up the stairs and bait the melee guys down stairs and use the counter method I talked about earlier, then when all the melee guys are dead shoot the ranged enemies. And lastly we have to most annoying wave, what you want to do is kill the two gunmen then kill the big icy looking guys with chain guns on the stairs, then grab one of the chain guns and run up the center stair to the back of the door and turn around and shoot everyone that comes up. All you should have left in this wave are some melee guys which you should kill using the counter method like before and some gunmen who you should keep your distance against and pick off with you plasma rifle. For the rest of the level when you fight against Mr. Sinister's D-list villains and eventually Mr. Sinister, use uppyb0t's guide above. Really hope this helps this level probably gave me the most trouble in the entire game.