Pretty simple rules here: pick a franchise.  Make your team from players that have played at least 1 major league game in any of that franchise's uniforms.  You may twist those players to any seasons of their careers.  There is NO LIMIT on the number of times a franchise may be selected.  If everybody uses the Red Sox, Yankees, and Cardinals that's fine with me.  Might be a little less variety, but it puts everybody on a level playing field.  You can announce what franchise you plan to use when you sign up, but that's not required.

A few nuts and bolts:
random alignment
no clones
no DH
no WW
trades are allowed AFTER your team has played 50 games; this rule is designed to discourage premeditated trades
50 LIVE required for the playoffs
you may have 1 team in each league but must use different franchises.