Well considering that Skype is mainly a way to, you know, contact people it doesn't seem actually insane to consider it.

Like many people, Skype is a fallback communication channel for me. I don't care if my brother or best friend is on Skype because I call them on the phone to talk, text message if I want to chat, or Facetime if I want to video chat.

I'd say Skype is a way to communicate with people, not a way to contact people. And for me, it's a method of last resort for people I can't call/text/Facetime/Hangout. I understand some people might say yes, but it's still somewhat deceptive to put this in the same category as "enable mic" and "enable camera", which Skype cannot operate without.

Skype should be a little more private than your cell phone number is. If I add someone's phone number to my contacts list, that DOES NOT mean I want them automatically added as my Skype contact.

Of course. But for them to ask doesn't seem like a dark pattern, since the main use case for the app is contacting people you know and it's reasonable to think most users don't want to micromanage different contact lists as you describe. The dark pattern stuff is more like when your app for rating ice cream flavors is asking for your entire address book.

I don't recall skype ever asking me for my permission to do this. I updated the app and then suddenly all my phone contacts were skype contacts and I had to go through and change the settings to never do that again and I had to manually delete each contact it had created.

To me this would be akin to facebook automatically adding the local chinese restaurant as my friend simply because I had their number saved in my phone.