I've known about the alt fire issue and frankly, have no idea how to fix it. In fact, I'm pretty sure Revolution has this issue as well, but don't quote me on that. Kinda know about the underwater annoyance as well. I tried working around that and not making those fights too annoying. Homing rockets are really useful there, but the ghost buster is good as well, since the beam lets you track your aim. But if that doesn't feel right, you can actually disable view bobbing in the options. I admit those parts might have been a mistake though.