Fallout 4 retconned The Institute

I'm surprised people don't talk about this more. Fallout 4 very blatantly retconned the established lore about the Institute. When you meet Dr. Zimmer in Fallout 3, the way he described The Institute is VERY different from what we see in Fallout 4. He talks about how The Institute has made the Commonwealth more civilized, how they have clean city streets and an organized Commonwealth security force to protect the peace. Not only to we see neither of those things in Fallout 4, but everything he says about The Institute and even the openness with which he says it very heavily implies that The Institute are the public and recognized legitimate government of the Commonwealth, and that Synths are an aspect of everyday life there. Them being shadowy boogeymen figures manipulating the Commonwealth wasteland in secret is 100% a retcon, and it's one that I think makes Fallout 4 make a lot less sense. Piper as a crusading reporter would make a lot more sense if she was chasing a government conspiracy and not a secret society. The paranoia around Synths would be a lot more potent and meaningful if Synths were a common everyday sight and the idea that the Institute (in this case, the government) is using them to replace people is framed as a crackpot conspiracy theory. The Railroad would make way more sense as an underground movement against the legitimate authority of the Commonwealth, instead of as a group of people who are super dedicated to Synth rights when the existence of Synths is shrouded in myth and mystery. It would make the Minutemen being a relic of the past make a lot more sense if they were portrayed as the peacekeeping force in the Commonwealth that was made obsolete by thee Institute's regime, and so only truly dedicated idealists are still members. The fact that we have a private detective in the story, a non-governmental investigator one could go to if the official authorities were untrustworthy... literally everything about the game's story would make more sense and be more impactful if The Institute were portrayed the way they were described before the retcon.