The thing is, without Mario, you cannot make this game. No one wants arcade baseball these days. If you do it with real players, people don't get it. It doesn't sell and no one buys. If you make an arcade baseball game with made-up teams and players like the old RBI or Baseball Stars, once again, everyone ignores it.
So how do you fill what is a valid niche that is definitely underserved without making a "generic" game? You put in recognizable characters that have arcade sensibilities and appeal.
Mario Golf: Toadstool Tour is an awesome golf game. It's not just good from a Mario/Arcade-style perspective, it's awesome as plain old golf too. It relies on your skill at playing it just like a good arcade/action/sports game should. With baseball, we really don't get that anymore. It's the real thing or nothing. Plus, Slugfest was just silly with its real players beating each other up on the field. That's just stupid. It doesn't work. You need the fantasy teams and players to make arcade baseball work and Mario opens that up to a whole different kind of audience AND to some baseball fans.
There's often been folks that lament the loss of things like RBI Baseball. Namco could never do superdeformed players in the US today and get any kind of sales. But with this, they have a great opportunity to put that engine to good use that can sell in any country.
I agree though that it would be cooler to have the characters in uniforms.