For question #1, there's a less complicated way to go about it. Create a Page field called "Favorites" (or "Subscriptions"). Templates allowed for this field should be: episode, series, and whatever else can be favorited. Add this Favorites field to the User template. Program the feature as needed.
For question #2, the approach you outlined is pretty correct and the ProcessWire way of doing things (or you could also use Options Fieldtype, but I don't prefer it). I personally call it "Options" instead of "Tools" and pluralize the option types (Languages instead of Language, Durations instead of Duration). Then create Page fields as necessary.
Jonathan Lahijani's post in Tools (Checkboxes, ..) building and Site-structure was marked as the answer