#1 - Context.
I think the biggest flaw with Subspace was it never explained anything or just left me asking too many questions. Who are the Subspace Emmisary, why are they attacking these established characters and for what reason? Now if the cutsey cutscenes did that I wouldn't complain but they didn't. The thing to establish is who the villains are. You aren't introduced to Tabuu until right at the end meaning you have zero investment in his character or just don't care. It's like how Satan appears right at the end of Lords of Shadow and I couldn't care cus I was invested in fighting the 3 Lords of Shadow to take onboard the "real villain"
I hate it when things do that, you have the villain established only to find it's just a red herring (Looking at you Iron Man 3 and Dark Knight Rises) and you got 5 minutes to establish the "real villain" when by that point, you're 10+ hours into the story mode to care.
The opening cutscene could have been how Wind Waker established itself. A simple tapestry showing the origins of Master Hand and Tabuu, how Tabuu wanted more power and seduced Wario, Ridley, King Koopa and Ganondorf to do his evil bidding. Then cut to the fight between Mario and Kirby. Not answering the questions left SE a broken mess!
#2 - Voice Acting.
I know Nintendo is afraid to give their characters any personality, but I think the whole mime ruteen stopped being cute around 2003. Mario Sunshine and Metroid Prime 3 proved you CAN give your games a vocal narrative without "ruining" what you established. It goes back into context, cutscenes help to set up a scene in games. Now granted you can set the mood without diologue. For example the opening to the original Castlevania sets the mood perfectly, however some scenes in SE could have done with a vocal narrative to explain what was going on. King Dedede being the prime example for I couldn't figure him out.
I felt he was a villain when I first saw him, then he acts all friendly at the end left me confused. I had to look it up online that explained what his deal was.
When I have to pause the game, hit up the internet to learn the story to the game I'm playing.... That's BAD story telling!
#3 - Cut the Great Maze.
Another problem was the needless section at the end with the Great Maze. SE is a chore to sit through alone and what I don't want is to basically play the same thing again but with more enemies and clones! Instead a simple Boss Rush Mode would have a vast improvement.
#4 - Cut Sonic.
His inclusion in SE was tacked on at the last minute and was very anticlimatic. Mind you I love the irony that the mascot of the company that tried to kill Nintendo ends up saving it
#5 - Give the game an ending.
It just stops when Tabuu is destroyed. I was hoping for some closure on the established arcs. Lucas feels he's become a stronger and more confident person from his adventure. Or how Donkey Kong settles things with Koopa for turning him into a trophy (cus we saw this with him and Ganondorf) maybe have Pit praised for his aid and have Snake and Sonic say their goodbyes before returning to their worlds.
Nope, just close on trophy shots.