I know that many of the skills available in game are down to playstyle but I've heard that training certain abilities, for example Swimming don't really provide much of a bonus and can prevent you from being powerful enough by the end of the game to perform some of the actions required (like hacking doors or lock picking) and can make the game more difficult near the end of the game.
Are there any of the other skills that I should avoid due to them being generally useless?
Are there any skills (other than my primary weapon skill, obviously) that I should definitely take?