The game ran for what, 7 years with newbies picking Controllers? I don't buy that argument at all, you can be a bad player regardless of what you're playing (Mr. Plants/Emp would have found another way to be awful on any other archetype, I'm sure). And weren't all archetypes available on each side following Freedom? There's no reason to make it "fair" with villains.
When game design decisions are made, they are generally consensus decisions made after reviewing all presented lines of thought and making the decision with the best support, not the one that is logically provably correct. Its logical for masterminds to be one of the locked archetypes because there were several points in favor (server resource utilization, complexity of play). Those points were weaker for Controllers, but sufficiently strong to make Controllers the odds on favorite of the original hero archetypes: on top of having similar points to Masterminds there was a symmetry reason for doing so analogizing Controllers to Masterminds.
Now, when you say there's no reason, of course there's a reason: there are lots of reasons. There are also lots of reasons to not do it. The question is, when you're sitting in a conference room with the rest of the dev team, and that train of thought is brought up, can you come up with a strong enough reason to not lock Controllers that will persuade your colleagues. What I can say is that "you can be a bad player regardless of what you're playing" is a completely ineffective response to "datamining suggests that Controllers tend to be harder than average for players to play." Its a true statement, but also completely irrelevant.
Players consistently erred in viewing dev decisions as if they were made by a singular hive mind. They tended to question decisions in terms of someone making a singular train of thought. The reason why Masterminds and Controllers were locked was because, in effect, those archetypes drew the most votes for being the ones locked, with different devs presenting different reasons for different archetypes, and those were the consensus choices. Sometimes, committees make decisions for reasons individual people don't, in particular they often make them for collections of non-overlapping reasons.
