I don't think it's possible to make a deep, isometric RPG for game pad use without redesigning a lot of core functionality. A great example is Skyrim. Great RPG and game in general, but the interface is absolutely terrible and the whole game feels "dumbed down." It's the same with Oblivion and Fallout 3. I'm pretty sure this is why Bethesda moved fallout away from an isometric game and made it a first person shooter. Action RPG's can get away with controller support because they have minimal environmental interaction.

Also, because the way consoles work is so pervasive, the elements used for a controller would ultimately spill over to the PC version. This is true of so many games (some are so bad, they force you to press specific keyboard buttons just to navigate the main menu, rendering the mouse useless).

Is it impossible? No. But I think the resources would be better spent making a fully polished PC game with additional content than a console port.

There is also the issue of co-op and the (possible) addition of full multiplayer support. You would either have to prevent cross-platform gaming, or shackle the PC version so the console players aren't always falling behind or (in the case of pvp) getting stomped.