I got a few ideas for the next Super Smash courses, here they are.

Streetpass Mii Plaza
Miis walking around a city, theme songs are from the Plaza, Find Mii, and from other minigames there, etc.

Mutant Mudds
A 3-layered course, which would be the only reason it wouldn't make it. There would be Muddsm of cousre, with themes from the levels and V or G land.

Dillon's Rolling Western
A level with Grocks in the background with Dillon defeating them, and the tough part would be the towers are occasionally firing at you.

Super Mario Galaxy
A somewhat simple course with you walking around a planet, which would be a sweet course, lots of oppertunities for theme music there.

They could modify Mario Circut to have some themes from MK7

Some new Kid Icarus course

8-Bit course
Changes from Mario, avoid the goombas and koopas and eventually bowser, to Zelda, to Metroid, etc, sorta like Mushroomy Kingdom, how it changes from 1-1 to 1-2

Bowser's Castle
Flames, thwomps, goombas, Koopas, Bowser, etc all trying to attack you, or maybe just the background, this course could go many ways with a lot of theme music possibilities.

Swapnote
An updated Pictochat

Courses to keep:
Warioware inc.
Mushroomy Kingdom
Mario Circuit
Smashville
Pokemon Stadium
Green Hill Zone
The LoZ courses
Lylat Cruise
The Metroid Courses
GET RID OF THE SOLID SNAKE COURSES!
And a few others I forgot.

Lastly,
for story mode, there is always a sort of movie showing how a character gets involved in destroying Tabuu. They should have another story, and with Miis, they should make a city with Miis walking around, just a normal day, just like on real earth, then suddenly, something apears in the sky and the sky turns red. Your Mii pushes through the crowd to get a closer look and then the screen says MII. Then your Mii runs forward to help whoever is already in story mode, etc.

I agree with super mario galaxy, but I'd also like to see a SM3DL course as well.
For zelda, maybe a location from ocarina of time for OoT3D.
DK country Returns course, of course.
Maybe a stage for Yoshi's story?
A metroid stage that could be similar to Metroid Prime 3.
A new starfox stage.
I was thinking a new Pokemon Stadium, this time with poison, ghost and dark elements.
They should also add a location from Pokemon Black & White.
A new kirby stage.
And a new earthbound stage.
Lastly they should make a new f-zero game for 3DS and use a course from that.

^Yes, they should^

I want a Bowser's castle level.
Trying to think of a new, better Kid Icarus level...

Yeah, bowsers castle would be epic...

What do you have against Shadow Moses Island? I thought it was a cool level. I don't see any reason why one would specifically want to have less content in something they paid for. That's like buying a box of chocolates, but telling the seller to remove one of the twelve from the box.

Hopefully they'll remake all stages from Smash Bros 64, Melee, and Brawl and put them on the Wii U version. Because I highly doubt the 3DS can hold that much, if they decide to actually make a 3DS version.

There will obviously be a stage of Skyward Sword. Probably in the sky or something. And I'm tired of all the Pokemon Stadium stages. I mean, sure it's a 'classic' to have it, but I don't really like them that much. Bring back a new Poke Float stage!!

Also, a new Animal Crossing stage would be awesome anytime in my book! Maybe we can get some Brewster and Tom Nook action...Okay maybe that didn't come out as planned but having them in the background would be cool (Sorta like Smashville).

A nice stage would be over the lake where you fight Hewdraw in Kid Icarus Uprising

Why not just keep all of the stages?

I think that they should just use new ones. Entirely new ones, other than Final Destination. It will show how much they think that these franchises hold appeal to their audience anymore. In other words, if they want us to know Earthbound, make a new Earthbound stage. Besides, I can only play Pokemon Stadium 1 so many times before I considering purchasing a weapon. Good God, they need to clean out there roster and start from scratch. The first ones I think they should develop:
One based off of Kid Icarus: Uprising as a showing that they still care. Preferably a multiplayer-based field or something.
One made for Metroid. If they still care about it as a core franchise, show us some good ol' handmade love!
One made for Mother 3. I can just imagine... Tazmily! In HD! #motherofgod
And finally one based off of Pilotwings: Resort. I loved that under-rated gem, and I would love a Wii U one. Yes, please!

Obviously there would be others, but that is my personal must-have list. Besides, they would all look good in HD and 3D.

I like the StreetPass Mii Plaza idea.
I'd like to see one that takes place in Shigeru Miyamoto's house. O_O Because I've been there before... when he wasn't there. And I love him.

Because some of them were pretty bad, and if they delete the bad Brawl courses they will have more space on the disc to make new better courses. Those were the ones I liked the most and should be kept, no matter what, but some of them were bad and they should make new ones to replace the bad ones.

Since the 3DS has a tiny amount of memory, either the graphics will make up for it or they have to do something...I think I got it: the 3DS version can play every single stage from the Wii U version, but it does not come with all of those stages, unlockable or otherwise. Confused? Let me explain: the 3DS game should have an extra space for a stage so that the player can download a chosen stage from the Wii U version to fill the void. He or she can choose his or her favorite stage and actually take it online! After that, the player can even swap one of the 3DS stages for a Wii U-exclusive one. That way, the 3DS version can actually handle the large number of Wii U stages to a certain extent.

That would be cool... but what if it were more like the Mario Kart Channel, where the channel is saved to the SD card and you can buy or download levels from the eShop and store them there then when playing Super Smash 3DS it can use the info from the Super Smash Channel so you can play those levels. Do you get what I'm saying?

Melee was on a 1.5GB gamecube disc, 3DS games can hit 2/4GB at the moment, if they go with 2 they'll probably have enough room for loads of stuff.
Brawl took up a lot due to the movies/audio/etc.

Hopefully the 3DS version just has a lot of different stages/etc to the Wii U version. maybe they could sell the others for each platform later.