Well the two bikes are quite different, I would say. I don't have a Ninja 250 so I can't make an exact comparison, but it seems to me that the Ninja is more sporty whereas the CBR250R is more a long distance bike (better fuel economy and more comfortable riding position (I have sat on a Ninja 250R at a dealers).
You need to decide exactly what you want from your bike, how you intend to use it.
