Ori,  
I don't know how feasible this is but here is my suggestion. I would like if, during the offseason, we could have an option to expand the roster like the NFL does -- maybe adding 3 roster spots. Then allow the option for multiple drafts -- maybe ones where the commish can set the parameters for the available players.  
For instance, allow the the commish to be able to set up a draft for only rookies in early July -- in addition to the regular pre-season draft. Then, when the time comes for the actual roster cuts, give the option for those rookies who have not yet been on an active roster to be allocated to a practice squad (maybe 3 players).  
That could be used in conjunction with the IR spot -- if a player goes on IR, the team has the option to activate one of their practice squad players. However, that player would then need to be flagged because he would no longer be eligible to return to the practice squad if he were on the starting roster (not on the bench) for a game.  
If the player on IR (if IR is based on the NFL availability projections of "Out', "Questionable"," and "Probable" and not really out for the season), is ready to come back, then a roster decision would have to be made as to who should get moved to make room on the roster.  
You could also allow the option of signing players from the other team's practice squads like the NFL does. If, however, a team signs a player off from your squad, I believe you should be compensated -- maybe with their 3rd round pick next season or some sort of compensatory pick.