Thinking about it you're right. IT was a proper deconstruction of an RPG genre. Instead of poking fun at RPGs it decided to highlight why we loved them. The story for the game was in the end a Story for a game. Which isn't a bad thing, it played with our expectations on how things are supposed to work out.
Plus the ending of Mother 2/Earthbound probably wouldn't be nearly as potent if it was in any other form.
Indeed. It's one of the reasons why I love the series so much. The games really felt like they tapped into the medium's potential for its storytelling purposes. Shigesato Itoi truly is a brilliant writer and it makes me sad that he apparently isn't interested in creating any more games.