Some of my own thoughts...
#1... Good idea... What happens when the counter gets to zero and there is still room left on the card? Does it say card full or can you continue shooting until the card is actually full? And just a note... The counter will report the lesser of the shots remaining on the CF or SD card... So beware of this if shooting different image types/sizes to the two different cards. It's not clear which card is the limiting one, so another suggestion is to put an indicator or offer a firmware option to select which card to monitor.
#2. This option is designed for shooting in AV mode in low light - and is a welcome addition - just the way it is (but having more shutter speed choices wouldn't hurt). If you need strict enforcement of shutter speed you should be using Tv or Manual. Also, attempting to set a shutter speed of approx. 1/focal is the default camera exposure programming in Av... We don't need a firmware option for it.
#3. Strange. I don't use wrap around, but I could see how this is annoying if you do.
#4. I don't find this to be an issue, but why not? I only use the 41 cross points which helps reduce the number of joystick operations required to move the AF point from one side to the other.
#1 - I have the camera set on "Auto Switch Card' and the screen shows the shoots left on the current card. I don't have time to look at the counter when the things go wild but I think / it seems that there is no negative number - the counter "improves" itself when it gets close to the limit. Most probably the algorithm is CounterNo = FreeSpace / FixedFileSize. The problem is that the FixedFileSize constant is a.) way off and b.) is not a constant, it is a variable (the cr2 & jpegs have compression). That's why a much better estimation is something based on global average (ie. TotalSizeShoot/TotalFilesShoot - and this number to be kept for each resolution / ISO) or much better on a moving average (the above number calculated only on the last 50-100 files).
#2 - Hello brother! 
A typical programmer response. ("This is not a bug, it is a feature") Sorry, but I don't think that 'broken by design' is a solution. 
See, we don't want to enforce a certain FIXED shutter speed. If I have a zoom, let's say 70-200 F/2.8, I simply cannot use Tv to set the shutter speed to... what? 1/200?? It is way to high in ever-changing light conditions. Remember we're talking here about an event handheld camera not a studio one. Yes, I know, IS. But I cannot think to Image Stabilization as a kludge for firmware shortcomings.
Another usage case: I have an UWA on the camera - let's say Tokina 16-28 F/2.8. Where to set the FIXED shutter speed? Based on common knowledge (and my tests confirm that) the lens deliver ultra sharp images even at Tv 1/16 handheld. But I cannot set it there because my subjects (men) are moving and hence, if the light permits, I want to have the shutter speed raised automatically and when they'll go again in the dark to lower the speed.
I use the Av mode but there is the same problem: the "approx" gives the blur of the image. We don't want the "approx" because this can be sometimes very "approximative". We need (imho) 'equal-or-greater'. And mind you, I found this issue by looking at blurred photos, not by nitpicking EXIFs.
Also, even if Av it would work I think that P mode is superior because it tries to get out the camera/exposure from the "dangerous zones" (slow shutter speeds AND open apertures) leaving you to concentrate on what to shoot / composition etc.
Because of all the above reasons, I humbly think that we need a firmware fix for it. Especially because it seems that it is a simple fix (they should change the test from something like "nearest value" to "equal and bigger ( >= )" if an option is set).
#4 - Thanks to validating me, but in fact it seems that you responded here at #5 
. The #4 is a very powerful feature which would provide multistage fallback exposure programs. Let me give you an example based on what I said above:
Reiterating the UWA case: In studio, the above lens (Tokina 16-28 F/2.8 ) deliver sharp images at 1/F and it has the best quality aperture @3.5-8. However in the battlefield, having a 1/16 speed usually produces blurry hands, legs etc. but even so you can catch a very expressive shot.
So, roughly speaking, I would have like this:
- Camera main settings: Av mode with F/4 - Auto ISO 100 - 6400, Min Shutter Speed: 1/60 (this is the best-case scenario which will cover 75% from cases)
- C1: P mode - Auto ISO 100 - 12800, Min Shutter Speed: 1/60 (here I still try to freeze the men)
- C2: P mode - Auto ISO 100 - 12800, Min Shutter Speed: Auto (the worst-case scenario: catch what you can)
...and in Super Safety Shift I would have set "C1,C2" - so if the camera cannot obtain the correct exposure with the main settings then it will try the C1 and after that the C2.
I hope that is clearer now,
J. Th.
A few more thoughts...
I think you can do what you want and probably get great pictures if you take advantage of the features you've got. Between the safety shift feature thats there, the control over ISO and min shutter you have, and the programmable custom modes, there's not a situation you can't cover. Don't be afraid to turn the mode dial once in a while
Speaking of mode dial... I'm surprised you shoot in P mode most of the time. Why? While I'm in no position to judge, I would encourage you to take more control over your photography... For example, I dont know a serious photographer that doesnt care about depth of field, and shooting almost exclusively in P mode says you dont care. It's very unusual. I can't imagine shooting anything but a test shot in P mode myself. While the 5D is a capable point and shoot, you're not getting the most out of it in P mode and as you probably know, wishing for more/different automation is not necessarily the best path to better photos.
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