I don't believe for a minute that the entire delay will be spent on the controller. But I do think that if they really are cleaning it up for a next-gen system, that we may see graphic improvements, as well as a more polished game (on both systems) due to it being given a good "proofread". (Can't think of a better word for this, really.)
It's been a hunch I've had for a few months, ever since the Xbox 360 came out. Rare had to overhaul two major releases to prepare for the Next-gen system. One of these titles, Kameo, has been in development since the Nintendo 64. The xbox version was almost ready for release LAST spring, but was delayed much in the way we're seeing Twilight Princess delayed now. It would not surprise me if the changes in Kameo since Rare was owned by Nintendo have given Nintendo some ideas.
First, check out this comparison shot of Xbox vs. the overhauled 360 version by Rare:
http://www.rareware.com/games/recent...kameo_14hi.jpg
Now, look at this screenshot of the horse battle from Twilight Princess:
http://www.zelda.com/universe/_pop/l...p?set=1&shot=9
Finally, compare it with this war-scene of Kameo riding through the troll army:
http://www.rareware.com/games/recent...kameo_08hi.jpg
Imagine Twilight Princess being cleaned up and refurbished to THAT level, and you can imagine that Nintendo might drool at the thought of doing it themselves.
Fact is, the advantages of going next gen would NOT be lost on Nintendo, especially since Rare used to be a piece of their own industry. If they can spice things up by offering some sort of dual-boot disk, it might further the interest in their new system while still keeping game sales flowing from people not yet willing to upgrade.
Also say little Johnny takes his Twilight Princess disk over to Billy's house to see what it looks like on his Revolution. That's when little Johnny starts drooling and asking his mom for a Revolution.