The issue is two fold. 1. Would it make a significant difference? 2. Dean has already submitted the content.
1 - I don't even agree that it would make a positive change in the tournament. There are multiple issues here, the first of which is the potential confusion to a team attempting to throw themselves together last minute. But in terms of whether or not its a good rule that would improve the experience, outside of the old "something different just to change things up" I see little merit in it. In fact, I think all you do is create a greater number of match up auto-losses.
Here's an example.
Team 1 - Dodonna Rebel - mass activation/shooter squad
Mando Armor Shooter squad with Mando CIO/Tact with Cloaked
Republic Yoda on kybuck Momentum squad
Team 2 - Dodonna NR/Ganner squad
OR Bastilla jedi interference build
Imperial Swap with Ozzel
Team 1 wins the first roll, looks at the squads, and has an extremely easy choice. They pick their Dodonna to match up with the Imperial squad since they can outactivate the swap (think Gencon Finals 2010). That leaves their opponents to pick their Dodonna against the CIO (not so hot) or against Kybuck (uh oh). Instead they pick OR vs the Mandos, hopeing that Bastilla can hold off the Mandos (tough tough match). At best that second choice is 50-50 when the first choice was 90-10 for the other team. The third remaining then, is still a 70-30 in favor of Kybuck.
You can do the same with any number of squad matchups, and obviously player strength makes a difference and so on that it's not so deterministic. As for whether or not people should be limited on Lobot - I find that silly. The figure is hardly a power figure, and most people use him to bring in mass activations when they want it (and they almost always go with this regardless). So you take away the option to counter the opposing squad match up at least minimally from 2 players - but have you done anything good for the game? Not likely. But you can say, "We changed it up".
Let's now consider the rules we've played under in the past. Was Dodonna abuse prevalent? Nope, sure wasn't. Was UH lobot? Not that I remember. People use him, but not every squad does so. I intentionally chose 3 factions above to eliminate the Dodonna abuse from being the central issue - to show that limits like this can create worse match ups. You could argue the same without considering Dodonna if these were the 3 factions/squad choices chosen in the current rules obviously. But the point is, the single faction rule already covers this a great deal. I like that people can be the "Boba Team" if they want to. And more importantly, I've never seen a compelling reason to add additional restraints to the format, and risk added confusion and difficulty.
As to my number 2 - I'm pretty sure he submitted it already