I feel its more the people rather than the games; every game caters to a specific crowd of people. MvC3/SFIV are more catered to the classic fighting game fans, who grew up on most of the old school mechanics, and are much slower-paced(Well...SF anyway). Games like GG/BB are are more differentiated and have way more mechanics than the previous games do: FD, FRC, IB, Burst, etc. etc. For someone who has been playing SF for years, going into something like GG can be daunting and not worth the effort.
And then of course, popularity has a large role here too; SF has been around longer, much longer and naturally the older members of FGC are mostly gonna prefer it. Most newcomers to the FGC are gonna hop on the Marvel bandwagon, without any real knowledge because its marvel.