The main realms that need work are remaking 3d assets for battle and field, battle is a bit more intensive, as there are a wider variety of monsters and bosses. Field models I have a system in mind that will speed up the process a great deal, by making some general assets and reusing and mixing up parts to speed up the process (aka no need to make arms that are the same with different characters) so we can set up color and model shapes to choose from, then just do new textures where needed. The other giant area that needs work is remaking the prerendered backgrounds. Basically you take the original background into sketchup, get the basics of the scene worked out, then put it in blender, rematch up the scene (in blender, set the background image as needed, then when in camera view, that image is overlayed, making it easy to line up the scene). From there you model up all the details high rez, do some texture work and render at something huge
Take your pick, let us know what you wanna do, and we'll let you know everything you need to get started.