After having finished it once, I tried playing with the "Second Wave" mutators, and MY GOD what a difference they're making. They're literally turning into the same scarefest as the original, aside from the alien-spawn/patrol mechanic.
Having a heavy hit a Muton and do 2 damage with a Heavy Plasma is truly terrifying (bigger randomization on weapon damages), but it's completely awesome to have a laser rifle oneshot the same muton with the next shot
Random rewards also cause some more choices to make when deciding which missions to follow.