Well the Season R/S Chibiusa did not know Uranus, Neptune, or Saturn so that suggests that one of two things happened. Either they died (and stayed dead) before Chibiusa was born or they did not become Sailor Moon's allies for some reason.
Of course yeah if we are talking time travel then you have to figure out Pluto's deal first. In S she has to be either the Pluto of the present or the Pluto of the future. Given that she knows Small Lady then I lean heavily towards her being Future Pluto. What does that mean though? Since Pluto was the one to bring Haruka and Michiru back to life that could mean they permanently died in the original timeline. That seemingly fits with what I said earlier about Chibiusa not knowing about them in the future. But then what about the third talisman her Garnet Orb? It had to be in possession of present Pluto...but we know she can't die or else she would never have become Future Pluto. So either it was not stored in her heart crystal or else the talismans were not all gathered in the original timeline. From the art episode we do know that Chibiusa's mother also possess the grail, so that more than likely means that present Pluto must have then gotten involved and already been in possession of the Garnet Rod. How that went down is anyones guess. Was she already active at ths time? Was this her re-awakening as a senshi? Whatever we just know somehow Sailor Moon ended up with the Grail.
As far as Saturn, honestly I lean towards thinking that Usagi would not have befriended Hotaru like Chibiusa did. I mean we are talking a pretty sizable age difference, where even if I could see Usagi being nice to her if she ran into her in the park...I don't see her really hanging out with her and taking her places on her own? Keep in mind that Usagi was also likely matured quite a bit playing mother to Chibiusa in R. So again would Usagi have really taken on that level of involvement with a strange kid on her own without that? Even in the final timeline it was usually Chibiusa who always had to ask to include Hotaru in things.
It was Chibiusa's compassion that played a role in giving Hotaru the strength to awaken Saturn inside of her, and it was Chibiusa's pure heart crystal that allowed Mistress-9 the strength to awaken. So without Chibiusa's super strong crystal to steal basically I am guessing that Super Sailor Moon the Inners, and Pluto found and defeated the Deathbusters before they could gather enough pure heart crystals to fully awaken Misstress-9. So then either they cleansed Hotaru of the weakened M9 or she died. Either way my thinking is that Saturn never awakened and she never actually became friends with the Senshi in the original timeline.)
(So my theory on what happened after is that at first when Chibiusa is sent back in S, that she messes things up because that meant the awakened Misstress-9 with her pure heart crystal but what was still missing was Souichi Tomoe. He was also vital to get through to Hotaru but he was still possessed by Germatoid in the timeline where Uranus/Neptune were still dead. So basically I think evil might have initially won when Chibiusa went back alone and thus Crystal Tokyo may have started to fade like in the Stars manga. NQS would not know what exactly what changed but knowing the time Chibiusa was sent back to train in figured that it was something regarding the awakening of the Messiah of Silence. That's why she would have sent future Pluto back in time to do everything she could including reviving Uranus and Neptune in order to prevent the Messiah of Silence from rising at all costs.)
S-Movie we are not talking too big of a difference other than Snow Kaguya would have had to be defeated without the power of Uranus/Neptune/MiniMoon in the final attack. Not a big deal.
For Super S...yeah I'm guessing Helios may have hid out in either Usagi or Mamoru. I mean he did know them in the past. I actually lean toward Mamoru since he is the one actually connected with the Golden Crystal in the manga and it is probably also the case in the anime based on him having a golden starseed. Plus to me with the impressive level of his psychic powers in the future as King Endymion (including power over Dreams!) it suggests to me that he more than likely does possess the Golden Crystal at that time. Furthermore as I see it following sequence of events if the golden mirror was in Usagi when she was attacked no one would be able to save her and stop it from being taken and her killed, but if it was in Mamoru, Sailor Moon would still be able to rescue him as once they had the mirror they would not have bothered trying to kill him since he would not have seemed like a threat. Either way with the mirror in Usagi or Mamoru that means it would have been found before they met and befriended the Amazoness Quartet. Which once again explains why Chibiusa again would not know them in the future. Anyways endgame would have then been a resolution much closer to the manga of Mamoru wielding the Gold and Usagi the Silver that would have ultimately sealed Nehellenia.
Super-S Movie yeah I have no clue. I mean for starters it was Diana who woke up Usagi to let her know all the kids were leaving. And it was seemingly Usagi who paged the other Senshi. Otherwise they would have seemingly only learned about the mass kidnapping in the city the next day and would have no clue where to look. It was Chibiusa who befriended Perle and made him question his beliefs and later her cookie that gave further strength. It was Chibiusa who provided Queen Badiane with enough power to complete her black dream hole. She also played a role in Usagi being able to snap out of her induced dream state... So yeah I have not the slightest clue where to begin to guess how events could have played out here but they were drastically different or else Queen B was time traveler herself so it didn't happen in the original timeline at all...
Without Uranus, Neptune, and Saturn (and also no Mini Moon...although she was not part of it in the manga was she?), Usagi couldn't have become Eternal Sailor Moon in Stars. Although would that have been a big difference? I mean I guess she would have just had to use her Princess Serenity winged form to fly to Nehellenia. Besides that though maybe Rainbow Moon Heartache or tapping into the Silver Crystals power directly could have been strong enough to cure the fake senshi until ChibiChibi upgraded her? In the Galaxia fight she didn't do much of anything besides use the Silver Crystal's power directly (a failed Power Kiss could have been any attack). Other than that without the Xenophobia of Haruka/Michiru an alliance would have probably been formed between the Inners and Sailor Star Lights sooner. I mean Sailor Moon was about to shake Seiya's hand to symbolize it when they interrupted. So information would have been shared sooner but I'm not sure that would have really made much difference. The Sailor Moon Galaxia fight would have likely gone down essentially the same just without the angst of watching Uranus/Neptune get killed in front of her.