Nintendo is not beyond experimenting with the series, and more to the point they made a solid commitment to delivering two installments of the series per generation. Thus far they haven't had one. So it is plausible that Nintendo initially gave the go ahead for Retro to do their own take on the series.
That said it is worth considering that the game was well into development when it may have been decided it was different enough, and the need for a new franchise was great enough that there was ample justification to rewrite the game as a stand alone. Given that it is Retro I think it isn't out of the realm of possibility that they could be developing a first party version of Oblivion.
Both Oblivion and Fallout 3 have been huge successes on the high definition consoles. Having a developer versed in the first person that also happened to be working on a fantasy game heavy into sword play would be an obvious leap.







