I would love to see Nights on 3DS. The 3DS controller would be great for paraloops. Although it seems unlikely, in an ideal world I would like to see a faithful remake of the Saturn version with an extra set of 8 new levels tacked on as a bonus.
Although the big wigs probably won't think it would be commercially viable, I reckon if done well it would sell loads. Nights has got a lot of love in the gaming press and the quick pace gameplay would appeal to handheld users, as you rightly point out.