Hm, I remember being annoyed with the submarine sequence the first time I played it, back then when I was...11?
But it took me a while to figure out that I had to activate all the controls, anyway...I actually liked this part a lot. It wasn't easy and getting the submarine to reach the gates of Atlantis required a unique understanding of how the controls function. My brain was mostly too slow to process what consequence the push of this button or turning of that wheel had.
The only arcade sequence I really disliked and found to be weak was the car chase in Monte Carlo. Because it felt nothing like a car chase! Wasn't compelling gameplaywise, either.
Oh, and Atlantis is great! Too bad that part isn't very replayable. :-/
