I concur with everyone else, definitely SuperS and StarS and they're honestly tied and are equally as divergent from the manga as each other, there's honestly no contest.
Though really none of the seasons of the 90's anime do a good job in following the manga, this isn't necessarily bad though. Junichi Sato and Ikuhara created their own unique work that brought interesting elements to the table and kept things fresh, for better or for worse.
I would say that when it comes to the 90's anime, probably the least egregious offender out of all the seasons when it comes to major changes would be S and don't get me wrong, even that season was plenty different from the manga, it's just when you compare it to all the other seasons:
Classic : Removal of mention of the Shittenou being Endymion's former guardians, reduction of Venus's role and removal of the decoy Moon Princess plot, removal of the Holy Moon Sword, addition of the Rainbow Crystal arc and Nephrite/Naru subplot, Princess Serenity's death is changed from suicide to just outright murder, everyone's memories get erased in the end unlike in the manga, the Moon Castle doesn't get revived.
R : Filler Doom Tree/Makaiju arc to rectify the memory loss situation from the first season, everything important regarding Sailor Pluto is cut and thus she barely plays a role unlike in the manga, there's an unneeded break-up arc, Chibs changing back from Black Lady is completely changed due to Pluto's removal, her awakening as Chibi Moon is moved into S, Diana's introduction is moved to SuperS, The Black Moon clan is made sympathetic and the entire reason for their goal is different, Ayakashi sisters get redeemed and live unlike in the manga, all the Senshi are around and only get kidnapped together all at once by Rubeus rather than picked off one by one and not rescued till later, Usagi is rescued by Mamoru from Demande rather than getting out herself.
S : Only real significant differences here is that Saturn's role in the ending/destruction of the Silver Millennium was cut and Tomoe lives and is redeemed. Oh also, no more romantic/sexual tension between Haruka and Usagi. Some stuff that didn't make it into R gets moved here too like Chibi Moon's introduction and Pluto stopping time and dying.
SuperS : Literally everything here is different from the manga
StarS : Same as SuperS, literally every element here is different, entire characters even get erased!
So as you can see when you compare it to the rest, S is easily the one with the least significant changes. SuperS and StarS are still the worst offenders by far though.