I'm sure one of the reasons to do this was to simplify the control scheme for console users since I don't see a gamepad being very useful at all in an isometric game compared to a mouse and keyboard but I could be wrong.
I think it has more to do with the demographic. Companies like Bethesda know their fanbase and what kind of games they enjoy. The console and the controller is not that heavily restricted that you can't get games to work which are ISO/Top Down. I mean games like Sim City existed already on the SNES and Command&Conquer Red Alert on the PS1. And it worked well enough. Like Furioso said, it depends on how much time you spend to make it feel right. But it should not be more difficult than making a first person game for the console.
However, if you want to reach 30 million gamers ... than you have to simply follow a certain design, mainly the lowest common denominator.
And I think that is the real reason here why we see this constant dumbing down. Bethesda probably feels that they won't sell as many games, which is probably true. But who ever said a game like Fallout would have to sell 30 milion copies to be a good game?