Pokemon Gold and Silver should be remade in a way that it would feel almost like an MMOG.
Also, Chrono Trigger should be remade, not ported, like FFIV. It would be funny to see a 3D remake of Super Mario Bros.
FFIX should get ported to one of the newer systems and it should get itself a sort of sequel...
Digimon World should get remade and should have the difficulty a little fixed... Sonic R should totally get a remake- New characters and at least 40 new tracks (since it only has 5... :/).
The Legend of Zelda should get a 3D remake, just to see how it would look like from behind Link's shoulder (or his eyes!). That remake, however, should stay completely like the original: less text, more exploration.
Super Robot Pinball should get remade where the enemies have more than just one attack... Actually, this would work on the DS since you could have the playing field in the bottom screen and a cartoon-like thing on the top screen, so each time either your robot or the enemy attacks, you see a real nice animation on the top screen. ...That might just use up the DS cart's entire space though! D: