Author correctly points out the elephant in the room for sources of unsatisfying endings with unresolved mysteries: adoptions of ongoing manga series (or any ongoing series, since there are adoptions of light novels too). The honest answer to his question is that I didn't think of it; I was more or less only focusing on things that were within the control of the anime creators.

Having said that, it's still the anime studio's responsibility to solve the problem. I can only think of two good approaches; the studio can break with the manga and come up with their own answers to the mysteries (call this the Full Metal Alchemist approach), or they can do their best to push the unanswerable mysteries into the background and focus the story on something that they can resolve (call this the Fruits Basket approach).

Both approaches can produce satisfying endings if done well, but I think that only the first approach produces a work that stands alone and has a real conclusion. With the second approach, I think you pretty much always get 'and then life goes on, with more happening' endings; satisfying but not complete.