While I don't generally dislike post apocalyptic game settings, I do think they could stand to have a lot more color in them. Fallout 3 was the best example of this out of the 6 I've played (FO 2, FO 3, FO NV, FO 4, Wasteland, Wasteland 2) and had absolutely no color.
But I think underwater levels are generally a bad call. It's just that's because game designers see fit to give your character perfect buoyancy. This would give you the chance to move in all directions. WoW fell flat when it introduced Vashj'ir in Cataclysm. It was an entirely underwater zone. But the problem was, there was too much movement to pay attention to during combat. Hitting the space bar raises you, but there's no convenient key binding possible that lets you drop. And it makes it especially annoying when you're orienting yourself against your opponent. Another thing that made it worse was that the level was too huge. Even if you cranked up the graphics to allow for the maximum draw distance, you could still barely make out anything because the water is obscuring any details that are far away.
The best way to solve this problem is to just let your character to sink like in the Metroid games. And just make the water a hindrance until you get some power-up. And the Gravity Suit in the Metroid Prime game even solved the problem of water obscuring your vision too!