I've had my Canon 5d II for over 3 years now, having gotten one a couple months after it came out in 2008. Still today it's largely without peer. Full frame, 20+ MP resolution, low noise, all for a little over two grand? Yes please. As a photographic tool it's just outstanding in almost every respect, holding it's own against a 60MP monster back in March. Overall I've been very very happy with it, in fact I just did a check of my total shutter actuations and I've apparently taken 76,627 pictures over the course of the 3 years. For someone who shoots weddings and events, that's a months work, but for me I'd say that it gives me enough experience to take another look at it's foibles. As I've said above, as a photographic tool, it's great. The image quality is terrific, usually limited by the lenses you put in front of the sensor. I've made big 30x48" prints that look fantastic even up close. Battery life is fantastic as well. I don't shoot a ton each day, but if I'm going away for a week's trip, I don't even bother bringing the charger and I'm rarely less than half full when I get back. Maybe there's room for even a little more dynamic range in the next revision, but then I'm just complaining to complain.
That said there are things that drive me nuts every time I pick it up. First is sound and speed of the mirror. I know it's a big chunk of glass and this is not a 1D body, but honestly, every time I press the shutter I expect pin, rod, or spring to come loose and pop out of the viewfinder. Not solid in the slightest. It wasn't when I got it and it's not now. There's also a pretty big viewfinder blackout where the mirror is out of position. Honestly, these two little things go a LONG way to making a camera feel more professional. Everytime I pick up a 1D or Nikon D3 I'm reminded of where the extra three thousand bucks must be going. And I had a 1Ds3 which I sold to get the 5D2. Very similar sensor, smaller size and weight, better screen, 1/3rd the price. It's a no brainer, but I still miss the feel of the big brother.
It's a little thing, but the fact that you can only do 3 shot +/- 2 stop bracketing is sad. Nikon cameras will do up to 7 shots at +/- 3 stops from what I understand. And this is software guys, it's not like it's a whole lot of engineering work to do. Give a programmer the morning to write the code and the afternoon to get the bugs out and then roll it into the next build of the firmware.
I find that tethered shooting is unreliable. The connection to the computer times out quickly and is hard to get going again. I've seen this both in the Canon software and using Lightroom 3 to do the work. In this day and age, that should be kids stuff. I'm not sure which side the problem is on, but it's annoying nonetheless.
1080p video is great, though I rarely use it. The 7D however can record at 720p at 60fps which you can then slow to half speed to do some slow motion work, however the 5D can't do it. I've heard it's a hardware limitation in some way, but annoying because the 5D should be the more powerful camera.
Speaking of the 7D I've got to bring up the 5D2's auto-focus. It's pretty bad. It was pretty bad and outdated when the camera came out 3 years ago, hell it was somewhat outdated when it was the AF system on the original 5D 6 years ago. The less expensive 7D which came out a few months later got an updated AF system which is a little embarrassing. Canon, couldn't you have waited a few months and gotten it into the 5D as well? It's fine for the most part, but in lower light situations it's useless. I'm a center focus point single shot user anyway so I rarely use the fancier tech but for the times when I've tried it I've mostly given up.
I'm sure there are more, but that's enough for now, I'll be sure to add to the list if I come up with anything. That said, there's not really any camera on the market within my budget that I'd rather use, so for an old camera it's doing ok.