I think you're overreacting just a tad. Calm down. Picture a sunny day and birds chirping in the trees. Go to your happy place.
First off, when you save and exit and the game gives you the "mission failed - user exit" message, don't take it to heart. Your save game is just fine. The next time you load your game, you'll be at the exact position that you were at when you saved the game. It's just the way the game is when you exit after saving. It means nothing.
Secondly, when you load up your save, you may see the lights flicker and hear broken glass. That's due to the way the game loads up the state of your submarine. First it loads your sub, then it applies any damage you may have suffered previously. Again, this is nothing to be concerned about. It's just the way the game loads.
Is it the most elegant system in the world? No, obviously not. Does it work? Sure, for the most part. I've had very few save game bugs crop up in my 4 years of playing this game.