Pretty much the normal stuff you'd look for in any used vehicle. IMHO, the 2nd Gens are better as there are numerous upgrades. The 2001 and early 2002's did have a number of engines that had oil consumption issues due to a new piston design. Not all bikes turned out to be oil burners though. For instance, my '01 has never had an oil issue. Those that were bad should have been fixed by Suzuki under warantee. In mid-2002, Suzuki went back to the older style pistons and the issue went away. Some folks do complain about the 2G S model's headlights being weak, but there are mods listed here that will cure that.
I would always recommend buying the lowest mile one you can find that's in your budget, but don't be too scared about mileage on these bikes as they will easily go over 100,000 miles with normal scheduled maintenance and several have gone >200,000 miles and are still serving their owners well.
Clutches typically get weak in the 50-60,000 mile range, so if you are looking at one with that many miles and it still has the original clutch, you can figure a replacement will be in the not too distant future.