Here are a a few very minor, nit-picky differences that I notice between the Nikon F2 and the Nikon F3
Back door release mechanism: I have big, dairy farmer hands and fingers. For me, the back door release mechanism on the Nikon F2 is easier to work that than that of the Nikon F3.
Light meter display illumination (in daylight): Outdoors, during the normal daylight hours, I almost always have a hat on to protect my skin from the sun. The hat blocks the little window that provides light to the F2 meters (other than those that have LED displays) but the hat does not block the window that provides illumination the the F3 meter LCD.
Location of the light meter light sensor(s): Light meter design involves making trade-offs. Every built in light meter design in every camera involves involves design trade offs - none are "perfect". This is the fundamental nature of engineering. It cannot be escaped. Specific to this thread, the Nikon F2 has the light sensing elements in the finder. The Nikon F3 has the light sensing element(s) in the body. This design trade-off results in many subtle differences between the two. For example, changing the focusing screen in an F2 may result in the need to also re-calibrate the light meter because the meter is measuring light coming through the focus screen. This is not an issue in the F3. There are several other non-trivial implications as well. (not pertinent to this thread but as an example of extreme design trade-offs, consider the light meter in the Leica rangefinder cameras that have built-in light meters...the light meter only works when the shutter is cocked and ready to fire! So, although the light meter is deadly accurate, it is only about a third as useful as it might be.)
The Nikon F3 finder is much easier to remove and replace than that of the Nikon F2....but this is of exceedingly little consequence to me as I very rarely remove the finder on either of them.
Light meter accuracy across the operating range: I've only owned one Nikon F3 but about 15~20 Nikon F2 (I currently have 5 Nikon F2 - one with DP-1, two with DP-11, and two with DP-3). Of the Nikon F2 I've owned, almost all have had the DP-1 or DP-11 finders. The meters in these use CdS cells. About half of these were dead or wildly inaccurate and the other half were pretty accurate but not accurate across the full range - they were off at the bright end or dim end or both. From the empirical evidence available to me, I conclude that this is just how it is with these old CdS light meters...at best, they were/are "good enough". As far as I can tell, the Nikon F3 does not suffer this type of error (again, sample size one). It is accurate across its full specified operating range - although it is impossible to see its LCD at the dark end of the range without clever application of additional, external lighting. Without accesory lighting, you cannot see the meter display in the DP-1 in the dark either.
Light meter "finicky-ness": The DP-3 and the DP-12 light meters I own (two DP-3) or have owned (one DP-12) have seemed to me to be a little finicky about ambient temperature and battery condition/ quality. They seem to really need fresh batteries - especially in cold weather - and seem to use battery much faster than the DP-1 and DP-11. So far, I've never noticed any such issues with the F3...and the vastly better F3 motor drive (reduced weight and cost, along with better ergonomics, and ease of use and improved reliability) means that it's not such a huge penalty to use the AA battery in the F3 motor drive to power the camera.
Film advance mechanisms: They're different. They feel different, They sound different. It is a very small difference and hard to quantify. I cannot say that one is better than the other but they are noticeably different. I will say that film advance in the one Nikon F2 that I had serviced by Sover Wong sounds and feels fantastic....significantly better than all the other Nikon F2 I have and have had. The film advance in the one Nikon F3 that I have is noticeably smooth and quiet but its stroke feels ever so very slightly longer than I prefer (the Sover Wong serviced F2 is about perfect in this regard).
Similarly with ergonomics. They both have superb ergonmics...but they are of course, slightly different. However, in terms of ergonomics, they are far more alike than they are different. Ergonomics are, of course, highly subjective. So, hold and feel and decided for yourself.
The Nikon F3 is slightly quieter in use than the F2...at least it seems so to me.
But for me, the BIG differences between the two make the Nikon F3 stand out as far superior to the Nikon F2. Namely, the integrated TTL flash metering and control, availablity to use aperture priority auto exposure mode, far better light meter accuracy and reliability, brighter focus screen and greatly improved motor drive of the Nikon F3 make it stand above my much loved Nikon F2.
All that said, I don't think you can go wrong with either of these. I keep, love and most importantly, regularly use both....and only infrequently use anything else and I have many other fine 35mm SLR to choose from. Most are packed away and do not get used at all anymore.