What lense were you testing that you had soft corners for? 16-35? 15 FE? 14?
Shooting with anything more than 21mm, corners don't seem to be an issue with the 1D series u/w. Since the 5D2 video mode changes ISO/Tv then Av last, it'd be wiser to shoot with a lens that is at least f4 and above to get DoF back.
With macro, to get back DoF, lights are going to be necessary and VERY powerful lights too. One method I managed to try was to have a white card to expose the subject but at -1.5 - 2 Ec. Then lock settings and use Ec to knock it back 1 or 2 stops depending on subject. As you say, when Av changes, the video gets funky. Another pain with the 5D2 that the AE locked settings reset once the 4GB limit is up, which means one has to be careful not to hit the limit but stop and hit set again.
Also users will also have to use CF IV-2 to switch AF-ON to AE-Lock for one of the C* custom settings so that when they shoot stills, they can switch back to AF-On functionality while u/w.
I shot the 5DMKII out in front of the shop (Backscatter West) in about 15 feet of water to try and do some testing in an attempt to have some scientific results. I shot it on a tripod with a 15FE and Light & Motion Sunray 2000 lights. Here's some of the tricks, tips, issues I had.
Focus in live view is difficult. I needs a lot of contrast, more than normal, to focus. I had to have my dive buddy (Russ) swim 2 feet out in front of the dome and put his bright blue dry glove in the center of the frame to get the thing to focus. After I did that, I moved the AF control over to *. I was shooting an Aquatica housing. I thought moving the control over to the * button was a really cool feature because I didn't want to accidentally hit the AF button again and ruin the locked in focus I had.
White balance was a challenge with a 15FE. I really needed a 3 sq ft white card! But I didn't have one and only had a small dive slate. Again, I had to have Russ swim out in front and hold the white card for me. The white card needs to be in the center of the frame when you take a shot to then assign the white balance from the shot as custom. The camera will take whatever for a WB, unlike video that will sometimes not take. What I though looked good underwater came out a little pink on my HDTV.
I had the Sunray 2000 lights at full power. Probably could have had even brighter lights. The concept is to nuke the foreground so that the camera will clamp down on the exposure, and darken the background. Most cameras in auto exposure mode tend to overexpose the background and underexpose the foreground. I found that the auto exposure on the 5DMKII was pretty close, but most times needed to go 1/3 to 2/3 underexposed on the exposure compensation. Going more that 1 stop up or down was way too much.
I tried to overexpose with a white slate to then pull it back with EC in order to get a higher aperture, but every time the exposure was more that 2 stops off and was too much of a pain in the butt to attempt to dial in to be practical.
I was getting apertures of 5.6 and 16. At 16, the ISO was getting a little high and I was getting banding in the water background. After I was done shooting and swimming in at the end of the dive I shot some kelp and got the lens to go to 2.8. Don't ask me how it got it to do that! The corners did look a little soft, especially at close focus. Still trying how to figure out how to get the planets to align and get a rhyme or reason for the F stop choices. I did notice (hope it wasn't a coincidence) that if I repeatedly hit the * button when the camera was pointed at the same lighting conditions that the camera cycled through different F stop and ISO choices for an equivalent exposure. Hopefully someone else can repeat this so I don't think I'm going crazy...
I'm going to shoot the crap out of this thing in video mode at the Digital Shootout in June. Hopefully I'll have more tips and tricks then.