Like Captain Marvel, I really enjoyed Thor at the time, but saw it fade away in terms of replay value. But where it considerably edges out Captain Marvel for me is in that, while it isn't the greatest story and may not have the greatest execution, it was incredibly important both in terms of setting up the coming together of the Avengers and setting the stage for the earth to be alerted to cosmic threats, AND in terms of Thor's overall, long-term character arc. With both of those things as context, I enjoy it on the rare occasions I revisit it. But that said, with all the quality films they have put out, I still put it down near the bottom.
I never had much of an issue with Thor 2. I would easily put it above CM, GOTG2, the first Thor, Hulk, and possibly IM2 and Black Panther.
But you know, again coming back to CM, I guess the issue I have with it is that it feels lower tier and right at home with the films I just mentioned. But unlike at least the phase 1 films on that list (and possibly GOTG2, although I think CM is a better overall film than that one), it doesn't have that important emotional character arc aspect going for it to elevate it a bit beyond itself. At least, not yet. But again, that isn't necessarily a "problem" for me either. The MCU has, overall, been fantastic, and I have no problem with every single film not being five-star.