I phrased this question's title as "Why has を been spared but ゐ and ゑ been deemed obsolete?"
Blunter ways of phrasing it would be "Why wasn't を deemed obsolete along with ゐ and ゑ?", or even "Why isn't を obsolete?".
(Personally speaking, I like the character を, but I don't currently think it makes sense that Japanese has it. Then again, many things in Japanese that appear not to make sense make sense after it's been explained properly)
Am I going over-the-top in avoiding offense? Is it ok to be blunt so long as I'm asking a question rather than saying "X sucks, right?". Or do nihon-jin take offense at criticism or perceived criticism of nihon-go?