MLB: from a players point of view they have a much better players union than the NFL.
Also, the way the owners work out their TV and Radio deals, insanely smart stuff going on there.
The players behavior, MLB seems to keep everyone under control and out of trouble (at least they keep it out of the media.
MLB, with the farm system in place it is much more professional. MLB seems to cultivate players up.
NFL seems to hire players similar to the pre-civil-war slave trade.