Congratulations. I'm taking the MSF course this weekend with my 17 year old son. My wife, who has a black 250r just like your wife's, is the more experienced rider and took the MSF course a few years ago. We thoroughly enjoyed the one ride we've had together. We're looking forward to a break in the weather so we can get out more.
As to moving up to a bigger bike, I've been told repeatedly by my friends who ride that I'm going to want a bigger bike by the end of the year. That's not happening anyway because of family finances, but I'm having such fun on my 250r that I'm pretty sure that I won't want to move up. That said, the bike I really wanted before I knew anything about the CBR250r was the ShadowRS. I found the seating position very comfortable. It's more upright than most cruisers. I don't know what I would move "up" to now, though. I really like this bike a lot.
I say, enjoy these bikes and your opportunity to spend quality time with your wife and forget about other bikes (and other women, too. LOL)