The stockers are probably alright - the biggest complaint with them is poor feedback and limited grip and surprising poor wear from a tire... many people have chucked a new set for something more fitting their requirements. Sounds like your fiance is getting comfortable on a bike so perhaps not such a bad choice... good thing with the 250 is that it doesn't wear tires down that quickly at all - sport tires will still last towards 10,000 miles.

Personal choice - the GT501... really nice tire for smaller or less agressive bikes.

Here's a link to the FAQ run down of tires for the 250...
http://faq.ninja250.org/wiki/What_ti...fit_the_250%3F

 

In the future, make sure the valve core is removed while you're trying to seat the bead...air will get into the tire alot faster and can overcome a lot of troublesome spots.