I feel he was treated quite good in the latter seasons honestly.
I'm the opposite, he at least had some semblance of a personality in the first 2 seasons (as jerkish as that personality was) from S onwards he became stale and felt more like a dad to Usagi than an actual boyfriend.
To be fair, he wasn’t treated fairly in the manga, either. He was the protagonist‘s Prince and loved one. He was brainwashed a lot. He was given some attacks and a chance to shine in the Dream arc—and that’s it.
To be fair, Mamoru as a character was always meant to be a reversal on the damsel in distress trope and the "token chick" archetype you commonly see featured in old Superhero stories. Sailor Moon, being the very feminist and girl-power series that it is played around with these tropes so in return we get a franchise that puts the girls front and center in power while the boy serves as "just the love interest" for a change.
Then we see him in the first part of R, memoryless, and while he's not as much of a jerk in that part, he's still not Mr. Personality, either. (What do Usagi and En see in him?). If the deleted material is anything to go by, a big part of the reason why he "chooses" Usagi is due to him regaining his memories...but what type of a choice is that if it's made based on his past life?
This is also something I feel the second part of R dropped the ball on. His excuse for breaking up with Usagi was valid (We shouldn’t date just because we were lovers in another lifetime) but it ended up just being an excuse and he never actually believed it it was just him wanting to protect her from a bad omen that turned out to be a test from his future self because...reasons? (I kinda liked that the DiC dub originally implied Wiseman was responsible as that would have made a bit more sense)
We kinda sorta see Usagi and Mamoru bond in the babysitter episode and the last two episodes of the Ail/En arc but even then its so underdeveloped we have no reason to believe these two would date if not for getting memories of their past lives and the opportunity to have Mamoru fall for Usagi for who Usagi is not who he and Usagi were was just squandered so bad.
This right here is why I could never buy them as a couple in the 90's anime and was always very "meh" about their romance in general. In the 90's anime at least it really does come off like Mamoru is only together with Usagi out of "destiny" and she wouldn't be his first choice if he had any say. A
Again, I really don't understand the double standards manga purists have. Anime!Usagi and Chibiusa bickering like sisters throughout the show's lighthearted moments gets picked apart, but Manga!Usagi saying stuff like "even if she's a child, she's still a woman!" in a dead serious scene doesn't.
As Clow said before, the difference is that plotline was used as an obstacle to help Usagi grow. Usagi is only 14 years old and was heavily sheltered both in her past and current life, it's heavily implied that Princess Serenity in particular was extremely immature (hence the suicide) so it should only be natural that Usagi would experience some negative feelings over the prospect that she's suddenly not front and center in everyone's lives for once, especially with her very first boyfriend who she just managed to get back from death and who had to wait over a millennia in order to finally be together again. Whereas Usagi's "jealousy" of Chibi-Usa in the anime is treated as just a joke and the same schtick keeps repeating itself over and over again for the sake of "humor." (You'll also notice in the manga, that as soon as Usagi deals with her insecurities and jealousies and gets over them she and Chibi-Usa never really fight over Mamoru ever again and she begins acting more motherly, showing clear signs of growth)
This is another thing that makes the Manga/Crystal version of the Black Moon arc overall superior to the 90's anime (again, except for most of the villains) Usagi actually grew and underwent significant character development. Were the pedophilic and incestual undertones stemming from Usagi's jealousy creepy? Undoubtly, but at least it helped facilitate Usagi's growth and she learned an important lesson regarding the forcing of love when confronted by Black Lady and Demande as opposed to the 90's anime where she was pretty much entirely stagnant as a character for the entire R season and learned nothing.