if the 90's anime followed the plot of the manga but also included filler which didn't affect much of the plot ... would it have been a better alternative for the franchise
I would rather die, good sir!
Okay maybe that's a little melodramatic and hyperbolic of me. I DO think there's too much stalling in the anime, and timewasting episodic moments we could stand to lose. But, by that thinking, it also sounds like we wouldn't get:
- Jadeite being punished by Beryl, instead of immolated by Rei; possibly no Thetis either
- The Naru and Nephrite storyline (as opposed to
that gruesome melting scene)
-
Maybe the subsequent Naru and Umino storyline (I guess this wouldn't affect the other plot enough so it might still fit; but seriously, this was such a great story and I'd be far less of a fan of the franchise if it didn't exist.)
- The Zoisite / Mamoru rivlarly; possibly not the Zoisite / Kunzite romance (as this muddles the vaguely implied Sen/Shi pairings from that one chapter cover and the later Casablanca Memories);
- The seven great youma in general (this affects the plot of the silver crystal's introduction heavily)
- I'm not sure if they'd have totally new from scratch arcs, so there is a possibility of no Ali / En / Makaiju storyline. Especially since an important reason for that storyline was the memory wipe at the end of season 1, another anime invention. (This approach might even strike the R movie from getting made...)
- The Ayakashi sisters accepting a plea bargain defection / recovering
- Saphir defying Wiseman
- Diamande trying to avenge Saphir
- Kindly, loving Professor Tomoe who is only doing any of this because he has to under durress, who is funny, cute, and a genuinely good dad, the nicest of all possessed bosses in the show, who keeps trying to help his daughter no matter what, and who survives... I mean, it's one of the best stories / most loveable character rewrites in the entire show, and it's completely incompatable with his manga personality.
- We would probably not get stuff like Minako stealing her own pure heart crystal, either, because while that doesn't have a lasting plot impact, it's a bit precocious if you're trying to stick to the manga's tone. Especially sure pure heart crystals might not exist.
- Mimete murdering Eudial and generally being a creepy memorable villain who gets an interesting comeuppance (ironically in Eudial's own device that she stole).
- Ugly baggage though it came with, Hawk's Eye's sacrifice for Fish Eye, and Fish Eye and Tiger's Eye's sacrifice to save Usagi; and the new beginning for them.
- Nehelennia making friends and starting over.
- The animamates being press-ganged heroines rather than jealous minions who stole the powers of other, long-dead heroines;
- Galaxia destroying the animamates personally.
- Lead Crow's "rivlarly" with Alluminum Siren; anger at Tin Nyanko afterwards; lamenting about amusement parks as she looks at her old photo with Siren.
- Tin Nyanko's half-healing recovery/personality whiplash.
- Galaxia's redemption; plans to put the star seeds back, presumably reviving the animamates.
Not to mention, you might also discourage wild new character development concepts, like Rei and Usagi's loving quarrels. The anime versions of the Sailor Senshi have quite a lot of personality compared to the early manga, in season 1, and if they'd been trying not to overstep their bounds we might not've gotten most of that.
There are so many reasons why, even though I do like and appreciate the manga, I vastly prefer the 90s anime. Many reasons. Yes, we could've skipped some stupid stuff like the long-winded Amazon Trio arc and it's unpleasant overtones; and the overall story could've been more succinct and focused; and, timing allowing, maybe they could've worked in the cool bits of Naoko's ideas that didn't make it into the anime, like the clearer backstory explanation for the Shitennou, or Sailor Venus and the sword, or Diana's proper introduciton; but
at what cost?! The anime's characterizations are amazing, and most of the times they cut loose with their own ideas, that's when Sailor Moon achieved true greatness in my opinion.
As for Crystal, what I would rather have seen is a hybrid continuity grabbing ideas from the manga and the anime. And I don't just mean the poses, I don't care about stock footage (that's something I could stand to lose in the '90s anime honestly, repetition is dull). I mean, why not glue together both versions of the Shitennou storyline at the seams, and things like that... both versions had some great unique elements, so I'd rather see something that tries to tie that together. (There's some things where you'd have to pick and choose incompatible issues, like Rei's wildly different characterization, but even so.)
So no, I will defend most of the anime's original choices quite fervently. It could be better, certainly, and the manga had it's great points that sadly got left in the dust- I certainly wish Mamoru had talked to the Shitennou's ghosts in the Black Moon Arc for instance- but the anime enriched the story in so, so many ways.
That said, I do respect the opinions of those who feel otherwise, and I can certainly agree that SuperS was deeply flawed and often bad.
Since there's no phages then they might use undead interstellar Sailors? 
