The best compromise would be a MLB license, but no player license. Set up MLB teams as "bosses" in a new career mode.
I'd at least keep the original teams and players around in some form, like maybe minor leagues, or maybe have MLB be the feeder league to SMBL.
I think there are a ton of ways to use the MLB license and keep the vibe Metal Head has. What happens behind closed doors, now that they are taking EA money? Well, that's where games become great or go south, and it is not always
just because the publisher screws it up. There is a lot of pressure, just like a free agent signing, to earn your big payday.
The things is, I love their version of franchise play a million times more than any realistic version I am forced to trudge through because realism. I'd rather them tweak their franchise play than try to emulate anything realistic.
I trust Metal Head a lot to find a really fun way to integrate MLB. But doing it via EA is a definite complication. But I can't blame them for taking this route. They put out three outstanding games, and built up a nice niche community. Now they get paid. Good for them, regardless of how SMB4 turns out.