The thing I'd change is remove Smash Run. Give back Special Smash and move Run and Climb to Classic Mode as Race to the Finish type games. Replace the entire Smash Run stage with the Temple stage from Melee or a "Temple II" and a few others. Replace Dark Pit's cloned moveset with a more original moveset. replace one of the Pikmin stage songs with a more intense remix that actually suits a fight. All I need are these changes and this Smash game would truly be the best possible one ever.
Edit: Or, make Smash run GOOD. Seriously, what's the point of choosing whether or not to allow Custom moves if the only way to actually have a good time with it IS TO USE CUSTOMS? At the very least there should be a difficulty setting. Or, maybe just a free run mode, or a way to adjust the timer. I HATE Smash Run. It's literally the only reason Special Smash isn't available in the 3DS version, it's such a large stage that could've been broken up into multiple little stages to fight on so I can have some larger stages to battle on. Change the enemy data to be preset based on Difficulty levels: MOSTLY weaker mooks at Easy, more variety at Normal, and mostly stronger enemies on Hard with a few mooks around. That'd be fun.
Or, maybe just maybe, even give me the Kid Icarus Codecs that are in the Wii U version! I'd like to be able to hear those myself, thank you.
Maybe I'd like a slightly more unique Dark Pit. The least you could do is give him a couple of kick moves. Forward aerial? a kick. Downward aerial? Falcon kick. Running attack? Falcon kick! Dark Pit is know to be kick-happy, LET HIM USE KICK MOVES! Speaking of, give Lucina the Melee animation for Shield Breaker. I get that she's a clone, but her attack power is balanced through her blade! It makes more sense to do so!
And also, Classic Mode. Change Classic Mode back. You know what would be cool? Having an Adventure Mode type of stage in Classic Mode. Fight in one location, journey onwards through hords of mooks (To give something of a story) fight another fighter, go onwards, fight Master Core.
Speaking of, that's another thing Smash Run could've been. The Adventure mode. Make it linear, and at the end throw in the Run stage as a speeding Obstacle Course before the battle with Master Core at the end.
Overall, my Pre-Edit post is pretty much the only plausible happening. Sakurai decided "**** it" halfway through so he couold make the Wii U version the better-in-every-way-shape-and-form version. **** you, Sakurai. ****. You. Trolling b@$#%@$.