In the late 1960s, a group decided which non MLB leagues counted as "Major Leagues," and the Negro Leagues were excluded, on the basis of race. They should have been included then. If they didn't do this for players like Cap Anson and others, perhaps there'd be an argument. They did, so there isn't.
It's really not going to change any career records (though Satchel Paige rockets up the charts, as he should have). This is obviously a huge win. These players came into the league and won Cy Youngs and MVPs, and unlike the USFL and ABA were excluded from the AL and NL rather than choosing to play elsewhere.