A few that popped into my head:
Regarding the '90s anime:
+ More scenes that flesh out Ami, Rei, Makoto and Minako's home life and their parents. We got a tiny peak with Ami, but I feel like it was a huge miss that we got nothing for the rest of the girls. Even if their back stories ended up being changed, it would have been interesting to see the 90s anime's interpretations of Rei's issues with her father, especially with her characterization being quite different from her manga counterpart.
+ More scenes revolving around Setsuna and Hotaru in general. They are shafted hard in later seasons, which is nonsense. I don't mind filler, and I think the '90s anime shines with a lot of its filler episodes. But when the series constantly chooses to focus on characters that appear only in one episode over the main cast... it's a problem.
+ Scenes that allow the audience to actually buy into Mamoru and Usagi's romance. While frankly I'm not a die-hard Miracle Romance shipper, and I think the earlier seasons do a better job at this, I think this is something that could be added onto SuperS easily.
Regarding Crystal/the manga:
+ Scenes where we get to see Ami, Rei, Makoto and Minako interact with each other more, especially pairings that we see very little of. It's kind of insane to me that across all adaptations, Ami and Minako barely interact with each other (not just the manga, but aside from correcting Minako's wrong puns, there's really not much in the '90s anime or live action series either). They're such opposite characters, but I feel that's what would make any kind of storylines interesting. You can also add the Outers to this equation to. For example, what is Haruka and Setsuna's friendship like? What does Setsuna think of Haruka?
+ Literally the majority of the villains need additional scenes to help flesh out their motivations. Even if you accept groups like the Witches 5 and Amazon Trio to be just the manga's equivalent of the Monsters of the Day, the manga's villains across the board just need a bit more time to develop. You don't even need to do much, considering Sailor Moon Eternal gave A LOT more characterization to Hawk's Eye in a matter of seconds.