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.