I spent a good number of matches playing against a pretty good ZSS player who blew me up at first, but overtime, I managed to adapt and picked up a few things. The first being that her grab range is deceptively large and that you can't really run away from her dash grab. She's hard to challenge in the air, but it's not impossible with proper spacing, and as far as I can see Nair as a defensive tool is useless in the air to air situation. If you get grabbed, it can lead to taking pretty big damage, but she can't kill you unless she gets the Bair or up B read and it's possible to escape both of those when you're at kill percents, the same goes with backthrow down B set-up. So if you are making the right guesses and DI then you could probably live to absurdly high percents. Also, if she misses with the Up B either because you fell out or it just whiffed entirely, then you can land first and down b punish.
The plasma whip isn't as stupid as it was in Brawl, but it's still pretty dumb, it semispikes and can push you offstage, I haven't been killed by it or anything, and it's not like it wins the match-up, it was mostly just an annoyance for me. However, when you shield it, she is punishable, I was able to get side B and dash grabs out of it, but down B might work too. On the ground you're mainly worried about when she will try to come in with the grab attempt, but you can short hop over the grab and the tether so spacing short hop forward airs might be a good idea against the ground game, in the air she has pretty good mobility with the flip and her air movement, also her divekick recovers fast so you have to be on point with the punish, but it's not completely safe or anything. If she's starting to charge her plasma shots then you can running shield it, preferably so you shield next to her then do a shield drop punish to rack damage or K.O, the recovery is pretty fast, and the full charged blast can't be short hopped over because of how Bowser's legs hang down when he's in the air, you can fair through it, but that's only useful if it connects because of the hitlag you get when it clanks. If she Down B's into you and uses the kick, not the footstool, on your shield. Then she appears to be punishable until a pretty lengthy animation after she lands, free Fsmash right there, so if you can bait that out then more power to you. For the footstool out of the flip, we can probably full hop Fair or maybe Upair OOS because she can't do anything for a short while after but you'd have to be fast.
Edgeguarding her appears to be pretty much impossible without mastery of ledge trumping or a really strong read, you can't safely intercept her at tether range because she can flip over you, and she has a stupid long tether reach that lets her mix-up her recovery timing and ledge options so you sorta have to be careful of the tether recovery but if you get the ledge trump, forget about trying to ledge drop back air, I'm not even sure if that's a real combo on anyone. Anyway, when you do ledge trump succesfully, you impose a mix-up on her, when I got trumps she usually flipped to get back to the stage. Ledge jump back air might work here since it would intercept the trajectory, however if you see her go low for some reason then you can just stand up and go for the charged down smash if you feel like she won't hit you with the up B. Now if she uses the flip to recover, then it gets a bit easier, the flip is rather predictable, so you can intercept it with a bair or dair depending on where she places the flip.
That's just my personal experience though, Hope this helps!