It is giving you a choice since you have more than one app that can complete that particular task. Select the app you "Always" want to use, and then IGNORE the message about "Clear defaults" (i.e. don't clear defaults when it takes you to the Applications manager) - which I agree is a stupid thing. In my case, I "Always" want to use the Phone to make calls, not Skype (just like your example), so each time it pops up when using a specific app which allows you to make calls from WITHIN that app, I select "Always" and that's the last time I have to do that dance for that app. Eventually, the occasions for the popup are reduced. just don't get hoodwinked into clearing all defaults, since then you will have to start all over again setting your default actions for every app.