Bottom line for me: The Subspace Emissary had a fairly interesting story and very very, VERY beautiful cutscenes. The problem is the gameplay itself. A sidescrolling version of the main fighting game is actually quite boring and repetitive. Sure they tried to make it different with obstacles every now and then, but overall it was still the same. It felt pretty empty having the story that it did. I appreciate the effort, don't get me wrong, and I recognize it. Like when they try to get the player involved in the cutscenes, a la the Porky statue chasing down Lucas, but there's only so much they can do with that.
I personally wouldn't like to see a Subspace Emissary pt. 2 in SSB4 knowing that it will take up room instead of more characters filling in. I know that the SSE is part of what makes the game great - wether people realize it, deny it or not - by giving it more diversity and an adventure mode that was made to be sort of seperate from the Brawl modes, but like I said, they tried, but they didn't really succeed.
If they want to make a Subspace Emissary pt. 2, they should make a SSE adventure game. I would like to see a smaller version of this come back in the next sequel to the SSB franchise, but I wouldn't want it to be so big that it takes up unecessary room when other players, stages, items, etc. can be included in the game. At the end of the day, people will be playing the Brawl modes (which suffered a lack of extra content because of SSE) and not the SSE.
I think it was fine for Nintendo/Sakurai and his team to try this out, but now that they did, they should realize that while it's fun, it's completely unecessary. They removed playable characters from the game, items, and even music!
I wouldn't mind seeing SSE pt. 2, just not at the cost of losing content from the main Brawl modes.