I have. I'm not 100% complete but I got past the great maze and Tabuu.

How many "extra" characters have you gotten?
I got Toon Link, the others are Wolf and Jigglypuff.

I got all the characters, all the stages, cleared all the events, and I'm still working on finishing the challenges.

I beat Tabuu and the great maze but I can't seem to finish off the rest of the Subspace Emissionary. Please help me I'm only about 80% finished or something like that.

in the boss levels, do you have to get their trophy to completely beat the level?

go back to everywhere there is a flag and get the orange/red cube.

Well some places I don't have a flag: Skyworld, Midair Stadium, Battleship Halberd Bridge, The Ruined Hall, The Canyon, Entrance to Subspace, and the Bottom left thing of the Great Maze.

Yup, that means you already got the orange box there.

Basically to fully complete a level you need to go through all the red doors in that level as well as collect all the orange cubes. This means that you need some very mobile characters that can access hard to reach places. Personally I recommend going through each level with either (or both) Pit & Lucario. Pit can just fly to hard to reach doors. Lucario on the other hand is extremely good at wall climbing so he can easily climb (or jump up i guess) tall walls and his up B covers a huge distance. Another tip for fully completing a level is to jump down all dark pits you see and if the screen goes with you just keep falling but if the screen stays in place then recover and climb back up.Basically just explore and spend lots of time on each level... from experience theres about 2 to 3 orange cubes in each level, so keep an eye out for them.
Sources: Im at like 95% on SSE
BTW Research Facility is hard to fully complete so that may take you a lot of time

i beat the storymode 90% complete all characters all events and 10 challenges left to go but they are rediculously hard so i gave up lol

Me and my bro are pretty good together and we started on very hard just for fun

Levels?

i haven't myself, but my BFF has!

im working on it...i started on very easy and intended to go up in level until i got to very hard or whatever. i still enjoy the game whenever i take the time to play it.

i lvoed subspace, then i wanted to play it again, halfway thru i remembered how boring it was

i dont think i beat it but i unlocked half of the characters by doing reg thing to start the event to fight em

(Don't be distracted read whats above then be mezmorized by my sig)
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i beat it

wanna know a little something, on all star mode, you knwo that thign you walk on to go to next level? well if you go over it with wario in a bike wheelie you won't go to next level

I beat the Subspace Emissary and unlocked all of the characters and stages. I beat all star mode on intense mode too, that was a pain.

I beat it and got most of the charecters except for Gigglypuff and Wolf. I got them later after that. Then I played it again and got board of it. One time is enough to play through that thing.