There isn't anything really upgradable for the ninja 250, but its a great beginner bike that doesn't depreciate much. Worth noting that it has been finally redesigned after a decade or more of looking a bit ridiculous. Its actually quite sharp now, if you like kawi.
I'm looking at picking up a Suzuki Boulevard 109R in the spring. My brother has one, and although he has blown the driveshaft twice, and the shifting is a little heavy, it goes like hell and makes a lot of noise.
The pipes, lights, and wheels would need replacing pretty quickly though.