That I totally agree with. I suspect a reason why they have not is that it might require a long overdue expansion of stadiums and roster sizes. But, at least on the latest consoles, there isn't a reason why it couldn't be easily supported. Still, particularly in Franchise, there is an artificiality in that player you put in A-ball don't even have statistical achievements, so other than the arbitrary overall attribute level and potential letter, there is no way to evaluate.
It in interesting that there are two A-class affiliates for each team (high A and low A). So, while it would expand from three to five levels, it would I think add realism to GM management in Franchise and also potential promotion options in RTTS.