I have always been and will always be a NCAA guy. But I think many people (myself included) see Madden as the big brother because it seems to get more attention in terms of press and advertising.
Additionally, Madden seems to get the "best" features one year before NCAA. Pro Tak would be the obvious example this year.
While I do not like this, I realize that Madden sells better than NCAA so it is a smarter business model for EA to give Madden more resources.