Like anything else, the more time you spend underwater the better you get it at. But it's like a different game. I like it because it reminds me a lot of space flight simulators I used to play. You are fighting in 3 dimensions. I don't find it that buggy either. Occasionally, yes, but not any more than most parts of the game.
The real issue with underwater combat might very well be profession related. Some professions are probably better equipped to deal with underwater than others. My first character that reached 80 for example was a engineer. With a bomb kit we're great underwater.
Also, Stacy, half of Orr and half of Frostgorge Sound are under water so there's plenty of underwater at the end of the game, including some of the personal story.