While I do enjoy some things about SuperS, I do hold that it's my least favorite season. Stars is quite a bit better in my opinion, although it suffers some of the same flaws and your mileage may vary.
My biggest complaint is the long stretch of overly formulaic behavior (Zirconia yells at trio; Amazon trio member picks somebody in a photo; creeps on that person in a suggestive manner; gets rejected, un-disguises, does the 1-2-3 routine with the table and the questionable imagery with the head-shoving and the giggling; Usagi and Chibi-Usa, who for some reason already met the victim probably through contrivance, show up just in time; Trio member runs off, tells monster to kill the victim for no reason with no followup; wacky circus battle; long double-attack scene of twinkle yell pegasus flashy thing moon gorgeous medizzzzzzzz; hasty wrapup and never speak of it again). This sort of thing happened to a lesser extent before and since in the show, but it's definitely the most grating here, because it is so overly similar that it's tiresome. The latter half of the season remembers how to have the villain plans not constantly work in a line-for-line pattern like this, and is much better for it, although Zirconia still stays samey and dull until near the end, which is a shame because she had a memorably creepy look.
And yeah, Pegasus is kind of an unlikeable chore to watch for most of the season due to what feels like the writers being compelled not to reveal anything useful about him until the last minute. The result is a character who's far too secretive, yet demands blind faith and support from others, which is yucky. Also, you're right that it's weird that Chibi-Usa keeps her involvement with him a secret for so long; both in terms of why (it's really yucky) and how (Sailor Moon takes so long to ask Chibi-Moon any questions about this pegasus magic and what she knows about it, but again, why?). He's still kind of interesting in the end- I sort of infer that he felt he was under an oath of secrecy, and failed to recognize Mamoru as Endymion until near the end?- but it's just sloppy writing I think.
Plus, another interesting weird thing somebody pointed out to me, which I'm inclined to see as an animation error- there's this blink-and-you-miss-it moment in the SuperS finale where we see what looks like Princess Serenity holding the golden crystal, except, Chibi-Usa's got it. Maybe it was supposed to be Nehelennia having a flashback to Queen Serenity, but as far as I know she shouldn't have had the Golden Crystal at any point either... so I think the animators / storyboard writers just screwed up on that one. It's so quick it's kind of up for interpretation, but it's weird in any case.
That said, I do like Chibi-Usa as a character (she's far from my favorite, but she's got good moments; especially in R), I'm okay with the dream mirror concept (what even are these soul macguffins that people die without, like pure heart crystals? I just take them as a genre conceit, like if the villain was stealing a portion of your brain or something, but it's pretty because magic), I like the last two episodes of the Amazon Trio, I like various random amusing bits (Diana's intro episode is pretty fun, or the Minako double date one), the Quartet are kinda cool (although they look quite ridiculous, but that's okay), and various parts kinda work. I don't hate SuperS, it just pales in comparison to the show's high points.
Stars does have some iffy logic, and it's own episodic moments (though it never drags on as long as the Trio arc.... I'm still ticked they got the longest villain arc, when there's so many better villain arcs unless you count- ah, nevermind), but I enjoyed it a whole lot more. However, nothing tops season 1 for me, and R an S are way up there too.
However, Stars doesn't feature the various recurring cast holdovers from the season 1 days (Naru- except for a debatable back of the head cameo-, Umino, Motoki, Yuuichirou, Rei's Grandpa, or Usagi's parents). SuperS didn't make particularly good use of them anyway in my opinion, but, it is sad to see them go since they were all pretty interesting in Season 1 and I think there was more potential there. Alas.
Also, Stars has an enormous case of skipping concepts from the manga, and several whole characters. So that's unfortunate too. I think it made good use of the ones it does bring in, though, and I quite like the Animamates in the Anime.