What you do as a freshman and sophomore typically improves by JR and SR year, as we've seen with a lot of QBs.
That progression was disrupted in TA's case, in large part because it wasn't just him learning the new offense, but the whole team. For example, I can think of several incompletions that were due to a guy running a wrong route - not because of a TA error.
My issue with the criticisms and my concern about this offense in general is that there are literally times when a correct read results in a wrong "decision." That's a very tough situation to put a QB in at the CFB level. I'm thinking, for example, of that third down play (think it was third down - may have been fourth) where he had a guy open underneath, but he also had a guy in single coverage on the outside fly route, which is considered "open" against that coverage. He chose the "hero throw" because it was the first read in the progression. Seems unfair to question his decision making in that situation, especially as a first year QB in the system.
I can think of anecdotal situations, too, but the fact is Tommy Armstrong was a 51.9% passer as a freshman, a 53.3% passer as a sophomore, and a 55.2% passer as a junior.
Not as much progress as you'd like, but progress.
And not exactly evidence that a demanding new system interrupted his natural progression.
I agree that Martinez progressed as both a passer and a game manager, even post-injury, but never overcame his ball-handling liabilities and never benefitted from a reliable defense.