The best deal that Alex Rodriguez might have made with Major League Baseball would have happened last spring, before Tony Bosch came in from the cold and agreed to be a witness for Major League Baseball. There were talks about a negotiated plea bargain then, deals put on the table.
If Rodriguez had agreed to something last spring, before MLB investigators had all the Biogenesis details from Bosch, Rodriguez might've been able to barter for a suspension for something close to 50 games, or what a first-time offender gets for a first positive PED test.
If he had taken responsibility then, owned up and made his best possible deal, then A-Rod probably would've been back on the field late in the 2013 season, with the whole matter behind him.