Common flaws are few as far as I am aware. The main thing is to keep an eye on the balance chain adjustment every 4-5,000km's. Apart from that regular servicing should be all it needs.
I put 65,000km's on a 1994 model and really didn't have any problems with it. The bike was a good platform for an outback tourer and still capable in the forests with a bit of modification. The biggest factors to look at when improving the bike are weight and suspension. There is a lot of unecessary bulk on the early 650's and it's dirt abilities are hampered by it. Reduce the weight and have a tinker with the suspension (cartridge emulators in the forks and possible a decent shock) and the bike will work pretty well in most areas. They are certainly comfortable on long trips.