I will agree that the 3DS' version of Classic is nice in that it doesn't force 5+ player Smash but the difficulty setting is on the Wii U version, just at the beginning which is how every other Smash game did it. Not saying change is bad mind you. Another issue with the 3DS one is how while yes, you do have branching paths and therefore choice, to my recollection, you only fight certain IPs on their respective stages. So if you choose to go to the Triforce symbol, you could fight any combination of Link, Zelda, Sheik, Toon Link or Ganondorf, you're also going to be fighting them on Gerudo Desert or...I honestly forget if the 3DS had another Zelda stage. The Wii U doesn't arbitrarily lock characters to the stages from the same IP. I'm not saying the Wii U version is perfect, it could've certainly been improved and there are certain qualities the older Classic modes have over it but I still personally think the Wii U's is the best.
Thing about that is, while the characters, stages, etc. are locked together in a specific franchise, the franchises themselves are also selected at random.
Personally, I think a way to solve the qualms everyone has with Classic Mode is to have different options regarding what opponents you battle, when you battle them, etc. We'll use
Melee's Classic Mode as an example; you go through various stages and battle opponents at random (for the most part), but the battle rules are the same for each stage (stage one is one-on-one, stage two is two-on-two, bonus minigame one, so on and so forth). There'd be an icon by Classic Mode which takes you to a screen and allows you to customize Classic Mode as you see fit. If you want the IPs to be selected for each stage but have the types of battles be randomized, like it was in
Brawl, or maybe have everything from the battles to the characters be selected at random, it can be done here. If we wree able to take it a step further, maybe you could be able to select specific characters and specific battle types for each stage, so it can be more like
Smash 64's 1P Mode.
Just my two cents. None of this is ever gonna happen but hey, a man can dream.