My guess -- and this is totally a guess from someone who is only marginally informed -- is that this is because MSU does not license through Collegiate Licensing Company (CLC). CLC holds the licensing rights for over 200 universities, conferences, and the NCAA, and a company like EA SPORTS can basically accomplish "one stop shopping" by signing up for a general license with CLC, and then offer logos, fight songs, etc. of the member schools to its users. If EA Sports wants to include MSU's protected intellectual property in their program, then they have to deal directly with MSU.
I did notice that Ohio State is included as a selection choice and OSU is not currently with CLC. That feature might have been created when OSU was with CLC, or maybe they figured OSU was big enough to license with individually. Notre Dame joined CLC only recently. You can be sure that when ND did its own licensing, EA SPORTS definitely got a license directly from them.
I don't know why MSU chooses to do its own licensing. I can only assume the University makes more money by doing things on its own. MSU was with CLC for a couple of years, but dropped out eventually. All of the other SEC schools are members, but several BIG and Big 12 schools have opted out.
