3GS will have no more problems than previously (== no problems), 3G will be no better: iOS4 is apparently significantly more memory hungry than iPhoneOS 3, which leaves the RAM-constrained 3G in a bad position. Many applications (including built-in) have come to be quite slow and laggy, and RAM-intensive applications (e.g. big games) have generally taken a turn for the worse.

4.0.1 doesn't look like it has much improved on the situation (apart from the psychological trick of "new release = faster", and the fact that freshly booted phones are less memory-constrained since Mail and Saf's background processes aren't running yet) so far.

Unless you need iOS4 features (or iOS4-only apps), i would recommend staying on 3.1