Thunderball > Goldfinger
Am I alone in this? I love Goldfinger and it is great, but I also feel it's a bit overrated as the Connery Bond movie to go to when talking classics. I think Thunderball is just as classic.
It really got the most of the best when it comes to iconic Bond stuff and Sean Connery is in his Bond-peak both acting and look-wise. Great villain in Largo. Strong and interesting Bond-girl in Domino. Great femme-fatale in Fiona. Cool henchmen. When it comes to classic Bond-characters this movie has some of the best. They have great dynamics and chemistry between them too.
It also has amazing settings and cinematography, the underwater stuff is unique still to this day. Great mix of the early spy-oriented stuff and the later more larger than life things. Love the overall slow tempo of the movie mixed with quick bursts of action.
The score is classic Barry brilliance. The humor is perfectly balanced wit without overdoing it. The editing and directing is also the best in the series. Very lean and careful.
And no, the underwater stuff is not boring, it's beautiful. The ending underwater battle is awesome. Terrifically shot, with a bad-ass Bond and with Barry's magical music. Same with the ending on the boat which is great and thrilling. Easily beats the Goldfinger ending on the airplane with Auric for me (and those effects looks sooooo bad even for the time).
My top ten Bond-films. Before Skyfall that is, I have a feeling For Your Eyes Only is gonna have to leave the list quite soon…
1. Casino Royale (10/10)
2. Thunderball (10/10)
3. From Russia With Love (10/10)
4. On Her Majesty's Secret Service (9/10)
5. Goldfinger (9/10)
6. The Spy Who Loved Me (8/10)
7. GoldenEye (8/10)
8. You Only Live Twice (7/10)
9. Dr. No (7/10)
10. For Your Eyes Only (7/10)
I have to disagree, as much as I am a Terrence Young fan and personally prefer his Bond films to Guy Hamilton's, Goldfinger is probably a better film. Connery was more on his game in Goldfinger. Sure, he wasn't visibly bored of the role in Thunderball like he was in You Only Live Twice, but it was clear that he wasn't giving the role the same attention anymore. He was phoning it in a bit.
On the looks front, since you brought it up, Connery wasn't quite as Bondian in Thunderball in my opinion. For instance, his hair piece/style wasn't as "Bond". It had a bit of a flat, combover look to it. In Goldfinger, his hair tended to fall into literary Bond's characteristic "comma" over the right eye, which was a big plus for me. Also, his Goldfinger suits are better. The Thunderball suits got a bit too trendy with the straight across waistcoat bottoms and narrow pant legs and lapels. Those fashionable features didn't seem to jive as well with the full cut of Bond's suit jackets.
Finally, there is the pacing issue with the underwater battles, that has been brought up before. That is the film's big weakness. The movie doesn't have the sense of urgency it should. As you said, you don't see it so I don't think anyone can convince you to see it otherwise.
By the way, I cannot agree with your rating of Casino Royale. I love the movie, but it is a very flawed film. The set pieces drag on far too long and don't quite fit the darker, gritty style the film is trying to establish. Overall, the film's pacing is uneven. To me, it doesn't stand on the same level as series classics from the 1960s like From Russia With Love, Goldfinger, and On Her Majesty's Secret Service.
EDIT: Gold Samurai, this Skyfall shot better fits with your series: