Increasing resolution means art assets have to be higher-fidelity, which means higher development costs. Nintendo wants to keep game development affordable across its ecosystem, but especially on its handheld device. That, price, and power consumption are the three main factors Nintendo is considering. I would be surprised to see a 720p screen on its next handheld, and astounded to see a 1080p screen. I expect we'll see something in the neighborhood of 480p or 540p for the main screen, and a bit less for the second screen. Don't expect them to ditch the resistive touch screen for a more expensive capacitive screen, either.