I'm hoping this doesn't happen to me. I've reinstalled Oblivion and am planning to do a new character and playthrough (I miss Cyrodiil dearly). I'm sure mods will help me through it, though. Oblivion has some amazing mods.
Plus, I think the key is to think of them as their own game, not in relation to Skyrim. Think of each game as standalone; each is a unique glimpse into a different province of Tamriel.