Main difference for me was the acting, with TNG losing out.
Stewart was great, perhaps the best actor of all the series. Spiner was OK. The rest of them couldn't act their way out of a turbo-lift.
OTOH, Shatner was, well, Shattastic. Nimoy was excellent and more--definitive. Kelley was really good when awake, and more importantly, fun to watch. Doohan was outstanding when given material. As for "the rest", well, Koenig was actually a pretty good actor, and Takei likewise. Nichols was surprisingly strong in her few moments. Majel, well, she was actually better in TNG.
I think you're giving Spiner short shrift, but what I really wanted to comment on was how dead on you are about Doohan. I LOVE early Scotty before they pretty much cut his balls off around the time of his first love interest.
Early on, Doohan plays Scotty with a very authentic (of course) military edge to him. I love it. There a lot of nice little things he does.
re: TNG. The Wesley hate was stupid. Beyond stupid. And once they got him in a real uniform, there was great potential for a relationship between him and Picard as seen in Wesley's final regular ep.
But the real diff is that McCoy-Spock-Kirk are FAMILY. The TNG are professionals. Hell, even Data's funeral has this air of "Shouldn't we be more upset about this than we are? ah well...I never was really close to you all."