I dont agree with most of what youve said, but I see your point.
I personally dont think he was being reined in or that he was somehow "better" or more aware of "societal issues" than before. The Metal Gear series is is a strange series that has drastically changed but also stayed mostly the same. Every game tries to be different, but always follows the same motifs.
I personally dont see the disconnect between MGS3 and everything after, mostly because I dont think MGS3 is the best one like everyone else seems to. At this point, it's a poor man's MGS5 with a good story to me.
For better or for worse, Kojima has always wanted to do more than the technology and budget he was using at the time allowed him. There's no doubt in my mind that if dreams came true his first Metal Gear game would have played like MGS5, starred Kurt Russell in his late 20s/early 30s, and would have had MGS4's cutscenes and neutered warring faction system. Sadly, that was not possible during the 8 bit days and their technological restrictions. Funnily enough, its STILL not possible because of budget restrictions. Making a game like that with the quality that he wants it would be ridiculously expensive.
Off the top of my head, MGS5 needed another big area, cutscenes rivaling those of MGS3/4 in quality and longevity, and good MGS bosses. So new character models, textures, animations, voice acting, gameplay mechanics, music composing and orchestration, and a shit ton of writers to write something decent. I dont think even another year in development would have covered half of that.
And im not a game creator, so maybe Im blowing things a bit out or proportion. I just assume its a shit ton of work.
To this day I dont think he's made the game he really wants to make. I have a feeling that every time he gets close he thinks of something better/different, and so he's constantly pursuing. It's why he keeps making these games. Thankfully, the foundation was solid as fuck, so what he builds on is always good.