I had the 800 Intruder for 5.5 years before I bought my Mean Streak and currently, my wife has it. Mine was the '96 as is her's now. I can only say one bad thing about it....when it's cold, it's very temperamental. Once it's warm, that thing will jump off a line like a jack rabbit. Yes, it does beat the 1400 off the line and in the quarter. I've ridden it through several states on many vacations and it has perform flawlessly.
The only other minor issue, and I do mean minor, is the tank size. At 3.2 gallons, it can be a bother if you're on a long ride and you have to stop every 120 miles, which is what I hit before switching to reserve. Then again, many riders stop around that time anyway and in your case, it's a toy for the city area, it may not be a bother.
A maintenance issue is the battery placement. It can be a PITA since it's entrance is from the bottom. You must connect/disconnect the terminals from the open slots on each side, then drop the battery down. When installing, you put it in, then make sure the cable's eyelet is in view, then insert into the post.
I can vouch for those with height. Though, I never gave the height issue any concern, until I bought the Streak, then I realized how small it was. The small size is a reminder when doing the maintenance on the wife's 800. The weight is about 450lb with full tank and you will feel a bit of push on a windy day.
As for the newer S50 compared to the 800, it was more of a name change than anything. Most of the bike is still the same. It's been a great seller for Suzuki which is why they keep in on the line.
The shaft drive is not an issue with me as most of my bikes have been shaft. They are the lowest maintenance of all three systems and fairly indestructible, but also lowest in torque.
Overall, if your size isn't a major concern or you are willing to modify it to fit you, you'll have a solid piece of machine, IMO.
As Wulf indicated, the Intruder Alert forum has a bunch of devoted riders and they are good people who will help you with any issue.