I'm probably not experienced enough with every MU on every stage to answer objectively, but if you want my personal opinion on what I like to play on, I'll definitely give it.
I'm personally fine with any stage, except incline stages and Final Destination. I feel like FD can be good for some MUs, like sword characters that don't have good projectiles, but no platforms, makes mixing up getting back on stage difficult. I also think it lets some characters with good aerials, get back to the stage a little too free. Platforms can help trap opponents, so the absence of them can make MUs very polarizing.
Incline stages, seems to mess up Phantom stuff, especially ledge trapping, and certain small characters seem to be able to camp and spam projectiles there. This is especially frustrating on Yoshi's story, where they're protected from the air, by platforms. I feel like zoners like Snake or the Links, tend to have an advantage over Zelda here. Overall, I don't like the layout of either Yoshi stage at all.
Based on my current feeling and experience, I'd rank them as follows:
Zelda Advantage
Battlefield
Pokemon Stadium 2
Smashville
Neutral
Kalos
Town and City
Zelda Disadvantage
Yoshi's Island
Yoshi's Story
MU Dependent
Final destination
Any that aren't listed, I don't know or forgot.
I feel like any stage that Up-Tilt can poke through the bottom platforms, is good for Zelda. It allows her to use platforms to trap landings, and safely pressure. I also think her power benefits from small stages.
I feel like Kalos and Town and City goes both ways. They allow for Zelda to push advantage hard, but allows her opponents to do the same. Both stages are wide or can become wide, so it makes it more difficult to trap opponents in neutral, similar to FD. The ledge and platforms make it very easy to do so however. So these might depend on MU and how good the Zelda player can handle neutral.
Probably need more experience to be definitive.