It's a real shame the submarine arcade sequence exists! You're the second person I know of who's stuck there so badly it puts them off completing the game, although I must say I didn't have any trouble. Fate of Atlantis is one of my favourite adventure games, although I've only come to that realisation quite recently.
You see, when I first played it, I played the Amiga version which was beset with an incredible amount of slowdown. I still persevered to the end, but the game was spoiled for me. Luckily I tried it again on the PC, years later, to experience it with speech... what a great game! Anyone who calls it humourless is being very unfair - it has humour, it's just dry humour unlike what you'd find in Day of the Tentacle or Monkey Island. Personally, that makes me appreciate the humour more.
If you're struggling to persevere with this particular puzzle though, maybe the game just hasn't grabbed you and you might as well skip it. I mean, you're closer to the end of the game than the beginning, and if it hasn't pulled you in by now, I guess it never will. Might be better to chalk it up to experience rather than ploughing through to the end and hating it.
On the other hand, as Rayvio points out, there are other routes through the game! I seem to remember the 'decision point' doesn't come too far into the game, so you could always nip back there and take a different path? For what it's worth, and having tried all the options, I found the Wits path to be the best of the bunch. The scenarios are more interesting, and not having Sophia around isn't any big loss.
Spoiler:You're reunited once you reach Atlantis anyway.
Anyway, good luck! I really enjoyed Fate of Atlantis, and I'd hate to see someone give up on it just because of one frustrating puzzle!
