RPG Maker XP and later are very flexible because you can actually use code and modify major parts of the game engine (you're limited mostly by the actual editor). But yes, in RM2K/2K3 your ability to break away from the standard JRPG framework is much more limited. Regardless, I've been surprised in the past with what people have been able to achieve within those limitations. I haven't played Ultima VII but I can't imagine it's completely out of the question, it just might require quite a lot of "innovation".