I sold my 2009 Ninja250 after getting the R3 and have ridden the Ninja300 many times over several years at the excellent family owned dealer and at festival demos. There are a few things I like better about the R3. The first thing I notice is that the balance shaft engine is really smooth. Much less buzz than the Ninja. Less tingle than an I4 actually, compared to the FZ6R or the CB650F.
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The second thing I like better about the R3 is the ride quality. The R3 is much smoother over wash board or rough roads than the post gen Ninja250 which tends to buck by comparison. The R3 has an uncanny long wheel base feel even though it isn't any longer and is just as quick to turn in. Being smoother makes the R3 the better sport touring bike for all day rides. It is a bit soft for the track though where rough changes to body position are more noticeable.
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And the engine makes way more power on the bottom end which makes it a better commuter. Cranking the throttle on the Ninja250 at 4,000 is kind of like, not cranking the throttle. Don't even get me started about the carbs on the catalyst Ninjas which never run right in temps below 45F. The R3 is also surprisingly better on gas even though it can make more power. The O2 sensor that the 49 state Ninja300's lack and large cat run really clean. You can warm the bike in the garage while checking the tires with no fumes. Don't pollute.
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The R3 seat is a bit soft but there is way more room around the tank for longer legs. I didn't notice the bars as being narrow. The plastic tank covers mean I need a new tank bag with straps.
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The headlights on the R3 are killer! The best pattern of any bike I've ever seen. Drop in an HID and there is still a perfectly sharp vertical cut off so no oncoming drivers can whine about glare even though you now have plenty of brilliant white light. The flash to pass button is trick as is the dash on a bike of this price including a gear indicator, programmable shift light and trip meter with fuel economy. They put a lot in there.
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I'm not a Ninja hater. The sticker on the back of my daughter's car still says Ninja Girl. But the Yamaha ticks more boxes for me than the Ninja300 and I was dissappointed to see Kawasaki drop the extensive demo program at the same time Yamaha and Honda are increasing theirs. So I am very happy to support the new bike in town and put my money where my mouth is on these light weight world bikes. And buy the R3.
To be fair, the Ninja 250 shouldn't even make an appearance in this comparison, as the 300 is a totally different animal.

I used to own a 99 Ninja 250 but man, the bikes are so different that I don't even talk about the 250 anymore. I mean, the 300 is fuel-injected, has bigger tires, a whole new chassis and instrumentation, slipper clutch, etc.
There's a lot to like about the R3. I think Michael's bike would have done much better (in our little acceleration test) if his bike had a full-tine and quickshifter.
The clips on the R3 felt narrow compared to my Woodcraft clip-ons, and maybe the R3 has adjustable clip-ons. Maybe not. It would be nice to adjust them and anyone can put aftermarket clip-ons on the R3 too.
The R3 looks and feels great. The tank is a little smaller (3.7 gallons) compared to the Ninja's 4.5 gallons but these bikes get at least 50mpg and as your own measurements indicate, are capable of 70 MPH+. You might need a break before your bike does but it's nice to have the choice to keep going on longer trips.
That Ninja 300 slipper-clutch is really nice. I noticed when I didn't have it, and most supersports and literbikes have slipper clutches. So, if you're used to it, the Ninja 300 doesn't disappoint. Otherwise, it's a good opportunity to practice rev-matching and clean downshifts.
All in all, I am super happy to see Yamaha, Honda, Kawasaki, BMW (naked 300 class), KTM and even Hyosung all in the 300 game. I think BMW will probably make a 'sportbike' variant of their naked G310R as well. It would be crazy not to.
All of this is good for us rider, regardless of whether we're just starting-out or experience riders who happen to love a small sportbike we can build-on.