If a player has no options he should not be allowed to be placed on optional assignment in AAA at the start of the year.  If said player played one game in the majors or was traded to a new team, he would have to clear waivers in order to be placed back on the AAA team.  You should not be able to keep talent indefinitely in AAA because you don't have a spot for him on the roster.

To fix this, create an optional assignment report like an arbitration report, which would occur at the same time as you are negotiating with your free agents.  You can choose promote to majors or waive, or workout a trade during this time with another team..  If the player clears waivers, he can choose to accept the assignment or he can choose to become a free agent.

I'm pretty sure that's similar to MLB.  

If I'm not mistaken, players with no options can't be kept on the 40 without clearing waivers first.   While that's worded poorly, I don't really feel an effort to fix it will matter.   It prevents teams from keeping players on their 40 for their entire careers without giving other teams a shot at them 7-8 seasons into their careers.

Nonetheless, have you figured out the repercussions of what you suggest to HBD?