As for me, got to say I like both ideas. I do think Stu's idea is sweet, but as you said it's basically saying the first three games never happened. I can see the pros and cons with both ideas.

Do like the idea in gameplay terms that the player gets a choice into which ending they want.

With that said, maybe for the get things back to normal ending, Sly does so by trying to make peace with Lucinda first so she doesn't try the "erase the cooper clan from history" plan again. XP