Option to never change status
A single option that tells Skype to never change the status from what the user last selected should be simple and would save a lot of headache.... Lots of people request that Skype stop changing their statuses. Others want the feature to automatically update you to Away if you're away or Active if you're Active. It shouldn't be too hard to have both.
If Skype wants to keep tweaking functionality on status changing, at the very least you should be able to click Yes to "Never change your status for you". If that is checked, then the app would never set you to Active when you log in if you were Invisible when you signed out. It would never set you to Away if you are Active but watching video or minimizing the app. It would never bring you back to Active if you were Away but wanted to reply to one quick conversation.
It doesn't have to work that way for everybody, but a single option for what is likely an easier implementation should be the bare minimum.