I'll add a bit to what Scott shared earlier. I would have to concur with his assessment that Peyton Manning's lack of arm strength was a HUGE factor in that game. Seattle's Defense as a whole (as you clearly saw) is a completely different kind of animal in terms of their sheer speed, athleticism, and instincts. They typically thrash weak armed QB's, as the Legion of Boom is just too darned fast and reacts with such stunning quickness that they generally tend to neutralize those kind of guys. Peyton is at the point of his career where that lack of zip on the ball is really going to cost him against a secondary like Seattle's.
Additionally, I'd also say that the lack of speed from the Broncos WR's as a whole (outside of Demaryius Thomas) really played a factor as well. Guys like Welker and J. Thomas just simply weren't going to get separation against the Legion of Boom.
And when you couple all of that with the kind of pass rush that Seattle showed they could generate down the stretch, it was pretty much going to be good night.
That said, the biggest single factor in that game (to me in my opinion) was Peyton Manning himself. What I'm going to say might sound a bit crazy to some, but in many ways I'd argue that Manning really cost the Broncos the game. I don't know if you ever saw that Sound FX Version of the game that came out (if not, you can PM me and I can send you a copy of it), but that was extremely revealing to me as you not only saw ... but could also hear what players were saying. Right from the get go, it was abundantly clear that the botched snap on the first play of the game really rattled Peyton. He kept harping on it on the sideline again and again -- it really bothered him -- and he stressed from that point (because of the crowd noise) that they were going to have to go with silent count.
It seemed to me like in essence that all week long Manning and the Broncos had been preparing for Plan A and expecting that Plan A was what was going to happen. After it became clear that Plan A wasn't going to work, it really appeared to me that Peyton was trying to scrap together a Plan B on the fly ... and really was unable to do that. What's additionally surprising to me is that for all the accolades that we heap on Peyton Manning -- praise him for being basically a coach on the field, a virtual football Borg that can recognize and adapt to anything -- is that he was seemingly totally unaware that Sherman and company had figured out his little "Omaha" tricks, all his little hand signals, and basically KNEW what play/routes were coming. Sherman and those guys were many times running the routes better than the Broncos receivers. For a guy with the reputation and pedigree of Manning to be seemingly unaware that they had figured him out (or was seemingly unable to adapt by giving them double counts or changing it up somehow) to me is quite shocking. How the heck does Manning not figure that out? It's undoubtedly completely and totally unfair, but I found myself questioning a lot of what I had come to believe about Peyton Manning. In this game, he struck me as a guy who if things go according to plan/to script -- he looks like a Hall of Famer. If he's expecting X and gets Y though -- he struggles to adapt on the fly. Again, that may be an inaccurate and/or unfair assessment, but based upon Manning's comments during the game, body language, and actual on field results that's what I would say ultimately cost the Broncos the Super Bowl.