I am using Magic Lantern all the time now on the 5D2 - it would be hard to go without it! For underwater, the two features I use most are the crop marks (I just used the Cinemascope crops marks for a recent dive trip). And the other useful feature is for MWB underwater. With the 5D2 you can get MWB down to just two button presses and no need to turn any knobs or take any photos (major PITA). I should note though that with my limited dives, I'm not sure how well their MWB performed so I thought that should be mentioned as it may not be aggressive enough for a typical 50' deep ocean water shot.
I have noticed that the camera is slow to "wake up" but at least all the settings are retained.
Oh yeah, I also really like their on screen focus aid. Quite handy. And I do like the summary data overlaid on the bottom (shutter speed, 35mm equivalent focal length, etc).
I just use the other little software program that formats all the cards in support of Magic Lantern and install the software on all the cards so its ready to go.
In a way Magic Lantern would be even better for a rebel series. The rebel series don't have the control wheel on the back. On this models Magic Lantern then can be set to us the up / down arrows for white balance and the left right buttons for ISO which saves more multi-button presses while under water. The 5D2 Magic Lantern can do this as well but needs access to the joystick which my Ikelite housing doesn't have but really doesn't matter.