I was also concerned about getting confused as far as the different controls on the scoot and motorcycle. I can tell you that it was not an issue and I assume that it won’t be. That being said, I haven’t been confronted with any sort of emergency/panic scenario; however, I don’t think that would change things as it’s not something I seem to have to think about. Maybe it’s because I ride both of them pretty regularly rather than riding one for a month and then the other. I know that when I got my current car, an automatic, after driving standards for the previous 8 years I kept trying to find the clutch with my left foot, but for some reason on the bikes it just seems to come naturally.
I am not trying to convince you to buy a scooter and motorcycle like I did, simply letting you know that that turned out to be an non issue for me. I went with the scooter first and think that was a good thing for me personally as it gave me a basic skill set and confidence when moving up. It does sound that at some point you’d like to have both and the one thing I would recommend is to make sure there is enough difference between your two rides. I think if you ended up with a Kymco 250 and a Ninja 250 the capabilities are similar enough that you’d end up choosing one that you preferred and neglect the other one. In my case, 150cc and 1000cc, the bikes are vastly different tools for vastly different purposes.