You are exactly in the same situation i was in when i was purchasing my bike (2012 cbr250r). I just actually got to test a ninja 300, so i felt what its like compared to mine. I know this is just an opinion, so take it how you want, but here it goes.
Looks - ninja 300 wins - looks extremely good, but the cbr is still pretty close
power - Its a tie in my book, The ninja has more power at the end of the range, but the cbr is much better in town. So it really depends on what you'll use it for. I know with the cbr, i can get to 75 very easily, and thats all i need to go.
comfort - cbr wins. Its a very comfortable bike. both are pretty upright, but the ergos of the honda are perfect for me, im 5'10 (180 lbs). Bumps are light on the honda as well compared to the ninja
economics - cbr wins, very good gas mileage. I tested mine out and im constantly getting between 65-75 mpg, depending on how i drive, its so much better than my mid 20's car
The honda also felt so much more solid. Everything was put together so much better and didnt feel cheap, plus being a honda, its crazy reliable.
Plus it helps that i know that in 1 1/2 years to 2 years ill be changing bikes (i wont say upgrade because the cbr250r is amazing) so i couldnt justify spending the extra. Although now im considering keeping the ceebee and just putting liability on it, its like 60 bucks a year and having a around towner and my commuter... Like i said, this is my opinion, and im sure someone probably thinks completely opposite lol