Ooh, ooh! I have an idea on how to get them to move! Shoot 'em down. Whatever is in that house has to be worth more than the lives of two annoying NPC's.
Anyways, to answer your questions about the menu:
-I don't know about a drop shadow altogether, maybe just more modern shading. As with all generations, the graphics are improved slightly, and with fewer limitations, I don't see how making the graphics a little cleaner (or at least just by improving continuity between the terrain drop shadow and the GBA "shadows on the boxes) would hurt. I do see your point about looking too photoshop-y. That's why I've changed my mind a bit.
-I put gradient in quotations marks because the intermingling of the two shades of blue on the boxes gives the optical illusion that there are more colors than there really are. I don't know how it will look, but my idea was that the individual boxes would look like buttons that you push up and down or plates (if there is no pokemon in the slot).
-Alright. Look below, in my crude cave drawing:
Say this is the bottom of the textbox
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB- That's like one row (pixel) of blue
_______________________________ That's the bottom of the screen