I’ll go out on a limb and say that the only 250 worth considering is the Ninja 250. Between a GS500 and a Ninja 250, the choice is fairly easy for most people, because although these two bikes have somewhat similar maximum performance, they have pretty different characters.
First you ask if you like the fully-faired racy look? I prefer the naked look for my first bike, so I went for a naked GS500. If you prefer a fully-faired bike, then you can still compare a newer faired GS500 with the Ninja and decide.
Then you ask if you prefer a lighter bike with a higher-strung engine (the Ninja), or a heavier bike with a torquier/more relaxed engine (the GS500)? Do you like to rev it like you stole it without going that fast (this could be fun or tiring, depending on your mood), or are you happier to putt along at lower rev?
Then you search Craigslist to see what’s available, what’s the best deal, and weigh your decisions.