Hello!
The disadvantages were designed to let the player squeeze out a few more points and to alter the game play. They were purposefully designed to scale horribly with the points they give. In general people should pick the disadvantage that they are likely to not face very often, so a person who picked "Pervert" should avoid Brothel work.
Incidentally, Greedy is actually one of the worst ones to take as it locks you out of taking the "pet" at the start of the game.
Flaws in general were designed to give a more customized play-through by upping the game difficulty. In fact, if you choose one of the starting presets when making a fresh character instead of using manual creation, none of them get added!