Subspace Emissary attempted to tell a story with bosses and cutscenes for you to play through as the characters all worked their way through the land to meet up at the final boss. I find it lacking, however, because you can't play Subspace Emissary all the way through as the same character. It's divided up and your switching characters or choosing from a few that are available for one part of the story before moving on to the next. So, it's not a cohesive complete journey like it is in Melee Adventure where the character you choose goes from Mushroom Kingdom to Bowser/Giga Bowser at Final Destination in the end.
Plus, Subspace is its own thing and universe with its own set of enemies and look. As such, it doesn't have that same sense of a Nintendo Mash-up like Adventure mode and Samus playing in a Zelda dungeon/cave beating up LikeLikes and Octoroks. The Subspace Emissary is foreign to all the Nintendo characters so Samus beating up the Subspace enemies doesn't feel silly, crazy, cool, what have you. It doesn't matter if it is Link or Mario beating up these enemies. They just aren't iconic of anything. Plus, the Subspace levels aren't really that interesting or highly creative. They're just simply things you move from one end to the other on beating up these enemies on the way. Adventure Mode had you running a lap on an F-Zero track of Big Blue while ducking for cover when the super face racers whizzed by as they zoomed along the track. The idea of hitting enemies with trophy stand bottoms to collect them is sort of like the Pokemon idea of capturing the monsters with pokeballs but it wasn't always that fun to pull off and was frustrating if you messed up and had to get some more trophy bottoms to try again. Thus, to me, Subspace Emissary was a step back from the future possibilities that Adventure Mode seemed to potentially have.