"I delete elements only when they severely interfere with playing." ...is what I chose, since it best fits my situation.
Generally, I don't delete anything - I just move them all into a new folder that I will create in the song folder.
I prefer the ouendan2 skin more than any other skin, so I usually remove the skins in the folders, as it actually bothers me if I don't see the skin. But there are exceptions, and sometimes I would leave the preset skin alone because it fits, looks good, and/or it doesn't bother me much.
I do have a strict policy though. Backgrounds showing anime girls in a somewhat seductive manner or any bg with a girl in it that I don't feel would be best for my family and others to see will be removed on sight. I maintain a PG-13 environment back home, and I don't want other people making assumptions or saying anything about me if they see a background like that while I am playing.