For starters this is NOT A PORT but really a remix if anything. The old game was NES and flat 2D based obviously. This one has the same basic story and territories but all redone in 3D. Furthermore the game has had the story somewhat rewritten as to add in personalities and relationships between the key characters of the story.
Visually speaking you are correct it runs on 1 screen, but just MOST of the time. When you're in combat they decided to go with 1 screen (the bottom one) for all the visuals. The team said that they wished to push as much as they could in visuals and audio to bring it up to a really high level of standards so they wanted to tap both processors to do so. As it is being used on the bottom screen the menus, walking around, opening stuff, and the rest can be optionally done with the stylus if you don't want to use the dpad+buttons to select attacks, manage items, etc.
I got this from the latest NP where they interviewed the team and then rewrote it into a good 4 page article talking about various things with the game. Of note many of the primary original creators of Final Fantasy from that era are working on the project including the main designer of FF3 famicom as well to ensure it turns out right. I have faith in this one being a solid title... and I do agree in the end it is of the visual quality of Final Fantasy IX(9) on there.