Ever the contrarian and turd-in-the-punchbowler, I'd say stick with your nice, low-miles '99.
This is my take on Gen 2s (my first KLR was a '08, my second an '09).
The '08 and '09 had a fair share of birthing problems. Nothing insurmountable, but the worst of it was their tendency to burn oil due to technical issues with the piston/rings/bore. Not the best choice for a Gen 2.
The '10 model year seemed pretty good and that carried on to mid '11.
In mid-'11 the clutch was changed to a short stack clutch, so the commonality in the clutch that had persisted since '97 was gone. In my mind, it is not arguable that the new clutch was in any way better. Other later changes were the elimination of the rear master cylinder carrier and incorporating it into the frame, the change to a steel rear brake pedal (eliminating commonality going back to '87). At some point, the carbs got nearly-irreplaceable fuel and vent nipples. There were other annoying changes that don't readily come to mind right now, though much of the changes were simply Bold New Graphics. Foremost in that was the 'Coma'
model that came out in a sort of Urban Camo motif.
It is true that the '14.5 model got some long-needed improvements in the seat and suspension department, but this need is well (better) served by the aftermarket. The improvements were decent and well-priced, but better can be had.
Were I in the market for a Gen 2 I think I would be looking at only a '10 or '11 with the legacy clutch. That's a pretty limited market. If I were simply looking for another KLR (presuming that I never find that cherry Tengai) I would look for a 2007. The black one.
Does any of this mean that the mid-'11 to '18 bikes are bad bikes? Absolutely not; quite the contrary. There were just enough niggling little deviations over the last 6 years of production that puts me off of them for the sort of stuff I'd like to do to them. They changed stuff that should have been left alone. This makes me of the opinion that the only Gen 2s I'd buy, now, would the '10 through mid-11.