Best thing to come out of the Federal League was Wrigley Field.
I agree the top echelon of Negro League players were major-league caliber, and the majority in the NeL were at least replacement-player level. Of course the problem we face is how do you correlate sketchy statistical records and word-of-mouth reputation into a set of SOM cards which are based on actual data?
You could generate SOM cards from the FL seasons - but they wouldn't be a "true" representation of the player's performance relative to the AL and NL.
The NeL cards we have are a noble attempt to place a value assessment upon their career stats, but they are of course a mirage. We can pretend they are completely accurate, but unfortunately they're not. On the other hand, it at least gives us something close to reality, which is all we can hope for. In my opinion it makes the simulation a much better product by including Negro Leaguers, warts and all.
The same cannot be said for the Federal League, for the very reasons rburgh said.