While the "Will GameFreak make a NX Pokemon game on time" discussion has been on for awhile, I do think there's a fairly big difference between DS->3DS transition and 3DS->NX.
DS had 150 Million units sold, 3DS has almost a third of that. Additionally, 3DS could play both Black and White and the sequel, NX is reported to not have BC so any further Pokemon release exclusively on 3DS would be actively repelling consumers.
NX is also a very important system for them, so being slow on the up take is likely not an option. I can see Sun and Moon skipping NX since its out 4 months before the system launches, but I would hope that they have started working on an NX title, at least the tech and making the models.
Not sure if Sun and Moon being an impressive step forward after a year of skipping releases is a sign that the tech is being put in use or if it's a worrying sign that they put a lot of work into a 3DS engine and they'd like to get more out of it.
I thought it would be interesting to kind of reboot the franchise with a remake of Red...again, but with better visuals, free form camera, maybe new combat, etc.
TL;DR:
Staying on 3DS has fewer benefits, does more damage due to lack of BC, and It's important for NX to have a good launch year