Zelda in general needs to expand it's mainstays outside of just Link, Zelda and Ganon(dorf) with the occasional Impa who's sometimes a badass ninja and sometimes an old fragile lady. If they could give Impa more story heavy roles as she had in Ocarina of Time and Skyward Sword, I think it would cement her role for Smash Bros., quite easily so even. Just make her use the naginata as her main weapon, and give her other distinct abilities and she's good.
Midna also would've been a great pick, only thing they needed to do was give her a second role. A sequel to Twilight Princess wouldn't have been a bad choice. They've done it for Ocarina of Time, wanted to do it for Wind Waker, and are doing it now with BotW2. But she missed her role.
Skull Kid also needs just ONE more prominent role to make him a Zelda franchise mainstay. I feel like he missed out in BotW as well, with the Deku Forest being back and all, would be ideal to have Skull Kid appear yet again. Seeing as Zelda games often start in a forest area, you'd think they would've found a way to implement Skull Kid in the stories yet again... But no. Then again, we just had a whole game with heavy Sheikah thematics, and Impa had a very forgetful role in that one.
I think this is the biggest issue with Zelda and playability in Smash Bros. Not even Ganondorf is a steady returning character as of late. Without remakes, his last role was Twilight Princess. Yes Hyrule Warriors too, but Smash totally forgot that game exists. It's great Ganondorf is seemingly back in BotW2, but he might miss out the next 10 games for it.