I love me the Nikon D3. It's the first camera that I've used where I feel confident going into any situation. The high ISO performance, huge LCD, dual CF card slots, 9 FPS, and 12MP files are amazing. Safe to say, Nikon hit a home run with this camera.
That said, I've got some complaints. Call it a wish list if you will. But after using this camera for about 6 months in a wide variety of situations, it's pretty safe to say that the tool isn't perfect. With the release of the D3x, I've come to realize that Nikon is advancing technology, but is clearly holding out for the next release to do anything drastic. I might/probably am too late to get into the D4 product cycle, but nonetheless…
What could be fixed for the Nikon D4
The OK button is useless. There are two ways to confirm a command in the menu system: hit OK, or hit the center of the 4-way dial. However, most things only require you to hit the 'right' button on the 4-way dial. The OK button, aside from being repetitive, is out of the wa I'd like to see a repeat of the D90's solution. Replace the 'push the center to confirm' option of the 4-way control with the OK button. This reduces clutter and makes menu navigating a more one-handed operation.
ISO input isn't always visible. God love 'em, Nikon has made the ISO on this camera kick-ass. I've got no problem instantly turning the D3 up to 3200 ISO. The issue is that I've got to take my eyes away from the viewfinder to do that. Oh, and I can't see that change on the top LCD like I can see shutter speed and aperture. I've got to go down to the bottom LCD. Now, this sorta makes sense because the small hinthint ISO button is right next to the bottom LCD. But, use the camera for just a few hours, and reaching for that button is as intuitive as looking at the top LCD to see what setting you're changing. Looking at the bottom LCD is not. The D4 oughta have a bigger ISO button and have changes visible on the top LCD — perhaps in addition to in the viewfinder would be fantastic. Movie mode. Yes, this is sorta cheating. No camera did movies when the D3 came out. But I fully expect video on the D4. It better. :) ← Now on the D3s!
No i-TTL built in. Okay, I get it. Pop-up flashes suck. And the Japanese think it's the mark of an amateur camera. Fine. I don't need a pop-up flash. What I do want, is a built in iTTL commander unit. Like an SU-800 built in. It would mean not having to carry a flash unit just to be a commander. That slims down on weight and makes the camera less bulking during use.
The focus switch isn't eyes free. Not a huge pet-peeve of mine; I can find the switch on the front of the camera to switch focus modes between Manual, Single, and Continuous pretty easily. Perhaps spacing out the settings (sorta like the markings would make you believe the switch is doing) so that we can feel when we go to manual.
GPS. This is a really old technology now. Nikon's even built it in to point and shoots. Why do we have to deal with this annoying dongle to get GPS on the high end cameras. Can we get something built in please? Even if the radio defaults to 'off' to save battery, it sure would be nice to have geo-tagging become standard meta-data that all cameras provide. (Let's go EXIF, you can update!) 
Face recognition and tracking. This one should be a no-brainer. Consumers like to take pictures of people, so Nikon et al has given them a focus mode that fines faces. The camera can then follow that face across the frame to keep it in focus and determine the correct exposure to make sure the people in the shot are what come out. What about this sounds like something professionals wouldn’t want?
The vertical grip needs a revamp. Maybe I hold my camera vertically more than other people do, but I’m sure the vertical grip isn’t as comfortable as the horizontal one. The big difference is the ridges on the bottom of the camera, which are meant to give some grip on a tripod head, and the back-end controls.
The ridges: Who uses a tripod head that’s the size of the entire base of the camera? Really? Isn’t it more important to have the grip be comfortable when you’re holding it — a far more frequent occurrence than putting it on a tripod — believe me. I’d like to some some texturing on the bottom, similar to the horizontal grip.
The controls: There’s an AF button nicely placed for vertical grip use. But there’s no AF/AE-L button. To use that functionality, you’ve got to use the one intended for the horizontal grip — impossible to do with one hand. (Oh, and while we’re here, that AF/AE-L button is quite a reach even on the horizontal grip, even for my large~ish hands.)
Bigger screen. OK, I’ve bought into the hype. Big screens are really cool. They let us actually examine the shot in the field — turns out that’s pretty valuable. I don’t know how much larger you can get the screen without cramping the buttons or the innards or the battery life, but … I promise to buy it a screen cover for Christmas!
Previews have compression!? Riddle me this batman: when you zoom into a RAW photo on the camera’s (very large-sized) screen, you see jpeg compression if you get too far in. I presume this is because the camera isn’t actually showing you the RAW file, but the jpeg preview embedded in the file. I’m not sure what amount of engineering is required to get around of this problem — I imagine a lot — but it sure is annoying to zoom in to check detail only to have it obfuscated by the compression. Don't have a photo of this (yet)
Don’t up the megapixel count! Weird right? Don’t increase something? Coming from me? I understand this is a pretty controversial view, but I’m a photojournalist. I do my photography light-and-fast. Quite frankly, a 12MP file is just perfect for my needs. It gets me plenty of resolution, but doesn’t slow down my post-processing much. I just don’t have the storage space/processor cycles to deal with say… 24MP images of the D3x at the rate I need to work. If a photog wants more resolution, then the D4x/D3x is where to look. Instead, how about keeping the D4 below 14MP and putting the engineering effort into bumping the ISO performance again? Think about this folks: a camera that goes into boost mode after ISO 25,600. Now, that, would change my photography a lot more than a few megapixels.
ISO settings are confusing. Further on ISO: when the bottom LCD tells me that I’m on ISO “Hi 1.0”, I’ve got to stop a second and do the math — I’m actually at ISO 12,800. Why do you do this to me Nikon!? I just want to know the ISO! I get the fact that you want to emphasize we’re in “boost mode,” but on the huge back LCD that has tons of horizontal real estate, why are we conserving space? Can’t it read “12,800 boost.”
Small complaint about the menu system. Nikon’s menu system has gotten much better over the years, it’s mostly logical, and despite the expanded number of options, it’s still pretty easy to find what you want. That said, there’s one command that Nikon buries: time-lapse. This admittedly, infrequently used option, is placed with the play controls — under an entirely different portion of the menu from everything else like it. Could it hurt to put it in a more logical place?
Switch to control the metering mode is in an odd place. I struggled to on wether to write this one up, because, I don’t find it to be a problem so much as an oddity. The switch to set the metering mode is located on the side of the prism, on the top of the camera. It’s an okay place to put it, because it’s something that’s infrequently fiddled with, but it’s not the only place Nikon's ever put that control. Instead of hiding it away on a surface used by no other controls and requiring you to bring the camera down from eye-level to make an adjustment, why not do like the D300, and have a dial around the AE/AF-L button? It’s not quite as easy to switch modes due to the dial’s stiffness, but that’s alright; at least then metering could join the big boys on the back of the camera.
A battery % meter. I gather the determining the actual % of charge a battery has remaining is a hard thing to do, prone to inaccuracy and a quick drop at the end of the charge. Nonetheless, we’ve seen it done often enough that it’s time for DSLRs to join up.
Built in dust reduction. The D700 has it. ‘nough said. ← Now on the D3s!
In camera VR. I promise, no puppies will die if Nikon caves and puts sensor-based VR inside the camera.
Thoughts?
I think, that's my whole list of notes, any thoughts/annoyances of your own?