I think it comes down to the gameplan that Hendo brings and his conditioning. Both guys have faded in fights but Shogun generally has the problem brought on by being forced into a grappling-intensive fight against larger opponents, Dan just sometimes isn't in decent shape. If Hendo comes with the primary intention of fighting against the cage and from the clinch and uses the threat of that shot or clinch to throw the H-bomb behind it, I think he'll win by late stoppage or decision. If he comes to headhunt and only headhunt, Rua's superior movement and outfighting will become apparent and he'll chip away until Dan is stopped late, likely by submission. The way that we the fans truly win, however, is if they both come to stand on a dime and slug because both have massive power and otherwordly Chins and it would inevitably be hellacious.
Dan is also on HRT - aka legal juice - so a lot of disadvantages a normal 40 yr old has are negated. If anything he has the edge in experience.
Shogun will win by stoppage IMO, he is too good on the feet for Hendo to deal with, even if Henderson does get a TD I think Rua`s BJJ is good enough to keep the damage to a minimum until he gets to the feet again. Rua by 4th rd TKO