I'll add my 2p's worth having had a '89 3.2 for two years then upgraded to a '90 964 C2 which I've had for 18 months. I would echo what others have said about making your choice based on your likely use. Sure there is less to go wrong with a 3.2, but if you will use the car as a daily driver and regularly sit in traffic then I would go for a good late 964. The power steering, bigger brakes, ABS, traction control (of sorts on the C4) and much better heating system just make it a better overall proposition for regular use. That said I used my 3.2 as my only car and it sat on-street in central London for 2 years, often left unused for 2 weeks at a time and only let me down once thanks to a dead alternator (and even then I managed to limp it to JZ Machtech). The 3.2 perhaps feels a bit more 'special' in a classic car sort of way, but personally I really like the looks of a nicely lowered and well sorted 964. Real world perfromance is fairly similar, though perhaps the 964's performance is more accessible due to much of what I mentioned above. As I'm sure you're aware most of the 'issues' with any 964 you will buy today will have been sorted, so don't be put off by that. The 993 is undeniably a very good package, but you need to decide whether it is good enough to justify a £10,000 price differential for a good example. Worth keeping in mind is that whilst 3.2 and 964 prices are pretty stable at the moment I think the 993 still has a little more depreciating to do, though I suspect it will always attract a premium over the 964.
I upgraded to a 964 as I thought it represented an easier platform to modify into a track toy, which I'm convinced is true (not that the 3.2 isn't very capable), and I felt that my 3.2 was a sufficiently good example not to 'mess around' too much with. Clearly if track use is not one of your considerations then this is not relevant.
So in short, no there's not a huge amount of difference between the two, but IMHO there is enough to justify picking a good 964 over a good 3.2 if you intend it to be a daily driver from a pure ease of use point of view. Though cost of ownership certainly is higher for the 964 even assuming the 964 requires no major work.
Jamie