To me Shatner is good but Nimoy was a lot more important to and contributing to the show ... his roles outside of ST were pretty meh so that may well influence me to not particularly like him generally or want to take his side.
I agree that Star Trek was Shatner's best work overall. As far as importance, that's debatable. The series was chugging along just fine in those early episodes with Spock as a more subordinate co star. He became more popular than anyone else, sure, but story wise, the series revolved around Kirk or Kirk's dilemmas for the most part. From start to finish. And in the third year, you can practically feel Nimoy checking out. Shatner is in there holding the series together while Nimoy monotones he way through the year. Unless he's given a reason to emote, he's less interesting than he had been in the previous two seasons. I am assuming he was already told by Roddenberry that Shatner was the star of the series and he was planning his next career step. Even in the late second season, Nimoy seems engaged but not in the final season. Shatner always gave everything.
That's in part because Shatner insisted that that be the case. While it's not impossible to increase status and presence, Kelly started out as also recurring guest star, as also being just a "day player", and through his work managed to get himself and his character promoted to main titles co-star.
Shatner was hired to be the star, was paid to be the star and got his 25%. Ergo, he was the star, regardless of audience preference. Unlike Lost in Space, the Trek staff didn't let the breakout character take over the series. However, Shatner wasn't one of the producers and, in the end, he didn't make major decisions and Roddenberry cracked the whip (in the long letter) when even Kelley got out of hand.
George Takei was never gonna be a bigger part of the show. Doohan, who was fired and then rehired before the series started filming, was a bigger character. Grace Lee was supposed to be a larger draw than Sulu. And remember, Sulu was intended to be the lead in "This Side of Paradise" but the production staff - not Shatner - decided that Nimoy was the better choice, both as a character and as an actor.
Kelley? Yup he did great and deserved his promotion. Shatner had no problem with that. Nah, they liked George on set and behind the scenes, but he didn't distinguish himself. He was fine, he was reliable. Not everyone can be the lead. And the 60's was not the era for ensembles.
EDIT:
@Warped9 covered most of that while I was typing but meh, I'll keep it.