I believe there are two reasons why Konami is making the bottom screen the primary gameplay screen for Aria of Sorrow 2.
1.) To contain (and ultimately defeat bosses) you'll be drawing magical spells right in the midst of the actual combat, on the main action screen.
2.) It's quite natural for most of us Metroid / Metroidvania fans to want to look towards the top of the screen for the mini-map. Looking up towards the top screen for the map isn't much of a leap from there.
That said, Aria of Sorrow 2 does seem to have some 3D elements and trickery for special effects and whatnot, right there on the bottom screen. Sure, it's not full 3D, but still. Certainly disproves the theory that the bottom screen is incapable of 3D.
Edit - Sho Nuff, the DS is powered by an Arm9 and an Arm7. The weaker of the two, the Arm7 is essentially the same CPU that powered the GBA, only THIS Arm7 is clocked at 2x the speed of the GBA's Arm7.