My first bike was a 2010 ninja 250. I could push that bike to its limits, around curves I could take it way faster than I ever could take my r6.
What is it? The weight of the bike? I know throttle control is a big part of it. I really couldn't **** up with 250 as in give it too much has or down shift and not rev match correctly. I don't know what it is I just cannot get this bike over.
Those two bikes are completely different animals - everything from handling, power, suspension, to smaller things like where the friction zone sits. The R6 has a pretty crappy power band for street riding IMO - works okay on track but with no tweaks the stock power band is pretty sucky for riding on the street.
Like others said, get the suspension set for you and the type of riding you do, that alone can make a huge difference, but there's still going to be a learning curve getting used to the shifting and power differences. I go through something similar each trackday since my streetbike ('05 ZX10R) and my trackbike ('02 R6) are very different. I spend more time on the 10 overall, and when I jump on the R6 I spend at least a couple laps just getting used to the bike again.
A lot is weight. There is a reason on a tight track with the right person riding a 250 or a motard can smoke most of the fieldon 600/1000 at a reg trackday in lvl 1-2. Less weight is later breaking, more speed, less fighting the bike etc.
I know it's partially me, just sucks, I feel like I had way more fun on the 250. I have had the back end slip a bit on the 600. That never happened on the 250. Which therefore makes me a little nervous.
Definitely setup the suspension for your weight. There's a how to in the suspension section, or bring it into a local suspension/race shop or go to a track day and have them set it up for you. That'll make a big difference. The stock setup is pretty wonky.
Other things to consider - what tires are you running? What pressures? What tires were you running on the Ninja?
What is the bike doing that kills your confidence? Is it hard to get it turned? Are you missing apexes? Is it running wide on the exit? Does it feel super stiff - like your riding a rigid frame chopper? Is it way too soft and floating around like a boat every time you hit a bump? Does it turn in / fall over way too fast and feel skittish?
What were the circumstances that you felt the rear slipping on the R6? Getting on the power? What was the temperature at the time?
There's a lot of details to consider. Things are a lot simpler on the 250, when you have a lot less power and can pretty much pin it without worrying about spinning up the rear tire.