Currently Spectacle puts the screenshots in the pictures folder and this doesn't look well organized. It would be better, in my opinion, if Spectacle saved the pictures in a subfolder called Screenshots.
No such subfolder generally exists, though. So Spectacle would have to create it. However this would make access a little bit less direct. Ultimately I think if you personally prefer for your screenshots to be saved in ~/Pictures/Screenshots, you should create that folder and set spectacle's default save location to that folder. That's why it's configurable. :) Personally I have spectacle set to save screenshots to the Desktop. Everyone's different.