They revisited McCarthyism in a 4th season episode called "The Drumhead" in which an overzealous prosecutor (actress Jean Simmons) tries to find some saboteurs. Since she is based on the left's idea of McCarthy, everybody is innocent and she eventually includes Picard in her "witch-hunt". Really pathetic.
Troi never really worked for me, but I guess she was no more out of place on the bridge than Bones was on TOS. I guess they felt the captain needed another sounding board.
The holodeck is described by Roddenberry in his plans for TOS, but they didn't develop it until TNG. It was kind of a lame idea, but they did a few interesting things with it. It usually didn't feature in the plots unless something went wrong with it and in merged into reality. One episode had a crew member who was using it to act out his fantasies with some of the crew members (something I could see happening). (The British comedy series Red Dwarf did a classic episode involving the merging of a virtual reality game in an attempt to root out a virus in their ship's computer in "Gunmen of the Apocalypse").
Even though the world of ST: TNG seems to be some sort of communist utopia, they made the Borg Collective into a nightmarish race that would fit in with any of the major 20th century commie regimes.
The show definitely improved after season one, and really hit its stride in season 3. There were duds along the way, but several really good episodes. The 2-part "Best of Both Worlds" featuring the Borg could have been a movie.
You made me think of Data, who reminds me of Rem from the ill-fated Logan’s Run TV series. The actor who played him was the only one who could act his way out of a paper bag. The difference was that Rem knew he was an android, and had no (simulated) desire to be anything else, and actually appeared almost more human as a result. Maybe I’ll give “Best of Both Worlds” a chance if I have the opportunity.
BTW, Bones didn’t actually have a permanent chair on the bridge, he was always walking onto the bridge holding something, but wasn’t elevated to a parallel rank but only the rank that came from being a skilled and committed member of Starfleet who earned James T./S. Kirk’s trust.