Isometric isn't being fair to modern capabilities, I think. Sure, the focus would be on a story or plot, but there's alot to be said about games where you can look around and see the world you're in. One of my favorite moments in NWN2 was when I logged on to a Persistant World server someone had put together, and saw just how beutiful a world they'd managed to make. It was awesome.
So please, 3D for whatever game it is. Could you imagine what it'd be like if you could play Arcanum now and literally get to look up and see the nascent skyscrapers as they streatch up above castles and old wizards towers? Or Sigil with the ability to watch it as it streatches up and around, then above you're very head?
If it was just an indie studio making a game for $10 a pop with a budget of $100,000 to start with before alpha funding, and with multiple aspects to the game so that the 'ground map' is only one part of it, Isometric would be fine (Xenonauts, for example). But this is Obsidian, the developers of the most awesome RPG I've ever played, and one of the reasons I love it is it's a 3d game.