I think you'd find that if you moved to SAAC for the U13 (and under) you'd find a HUGE difference in focus. I say that as a former Rep Coach in the Club system. For me, it has been a terrific and eye opening experience to see the difference.
Even Refs will comment that you can tell the difference between parents in a SAAC program vs a Club team. The SAAC parents are (usually) not coaching from the sidelines.
Trying to be objective, I think that at the younger ages if you have a kid playing for a SAAC team 3 x week, they would be much further ahead in their development than playing with a Club Team + 1 night a week with TFC-A. Once the OSA's LTPD model takes hold, we'll see. That new OPD League will be another interesting development as Clubs will be required to adopt Academy-like standards in order to participate in the top tiers.
If you have 20-25 clubs and SAAC members offering a training focus (3:1 training to game ratio), qualified paid coaches, a focus on individual development, therapists, etc... how will TFC-A compare to that? What would make them different, aside from the cache of their name?
As for the older guys, I think SAAC and TFC-A are offering similar options. More emphasis on training and emphasis on paid, quality coaching. That said, I have no idea what the coaching credentials are at TFC-A. Brennan was rumored to have his B license. Being a former player doesn't sell me on either SAAC or TFC-A. I want quality coaches
As for more MLS options, I'm not sure. Take 2 Provincial players of similar skill. One whose MLS rights are held by TFC-A and the other who hasn't signed with anyone. The TFC-A kid can only go to TFC unless they choose to send him somewhere else. The kid who is effectively a "free agent" has the option of Toronto, Vancouver or Montreal... assuming they want him. He could also go without hassle to the NCAA. I'm hearing TFC-A kids can go too but it may be a little more complicated given the "commitment."
I think of a kid like Aleman whose rights are now with Vancouver. If he ever wants to come back he is at their mercy so to speak. If they have no plans for him on the first team, he's stuck until he can finagle a release/trade.
The free aspect to TFC-A is certainly eye catching. But if they can't offer development better than SAAC (and the upcoming OPDL) I'm not sure that it is an advantage.