Ya, having Amedola and Edleman on the flat and Gronk and Lafell on slants really helped the Pats to be able to disguise the routes(with different formations). I was trying to think of a way for the Broncos to do the same, but they just did not have the players for it really.
Styles make fights as they say.
/Seattle's weakness in the secondary is against smaller, quicker receivers(Sanders,DJax, TY Hilton)
Thomas and Decker's style plays right into their hands, plus their d-line was better last year.
Pats' offense doesn't have flashy skill players, but they consistently get 3-5 yards on first down and set themselves up for third and short better than anybody and it's due to these short throws and receivers like Edelman and Welker previously being difficult to tackle so they always manage to get that extra yard or two. Add that

is the best at identifying advantageous matchups and exploiting them and it's curtains
Broncos offense would consistently get into 3rd and long situations where against the elite defenses you're much more likely to fail.