Totally agree with your assessment of this season. I thought it was better than last season for sure on a number of levels, and ultimately better for both Eve and Villanelle as characters, but they got lost in their own show a bit.
And I agree that the show needs to re-center Eve--she got particularly lost in the sauce this year. Last season, Eve was still very much at the show's forefront, but the writers had no clue what to do with her so they basically just replayed her S1 arc. This season, the writers had a much better grasp on what they wanted to do with Eve--not only processing what happened in S2 but have her give up once and for all the "normal life" she was clinging to, admit her own culpability in what her life has become, and embrace her new life (because this new life is really what she wants if she is honest with herself)--and the season started out strong for her in the first 2 episodes, but her arc faded into the background when Carolyn/Konstantin got foregrounded and Eve's own investigation into Kenny went exactly nowhere. I applaud Sandra Oh's lack of ego about the show but Eve and Villanelle need to become the real drivers of the show and narrative again, not Carolyn and Konstantin, and Eve needs to be the focal point of the show.
I do think one structural problem the show had this season is that it wanted the Big Four to be at loggerheads with each other, but that meant it had to invent a bunch of secondary characters to have the leads interact with, which just diluted the story. Villanelle had to have Dasha and Helene, Eve the Bitter Pill crew, Carolyn Geraldine and Mo, and Konstantin I don't even know--he ducked in and out of everyone else's plotlines. I don't know if it's possible, but the show needs to either have the leads working in tandem a little bit more to cut down on the secondary characters OR just don't feature Carolyn and Konstantin as much if you don't really have story for them (ahem, unnecessary Geraldine plotline; Irina's stuff also kind of fizzled).
Re: Villanelle, my interpretation is that it's a combination of A, B, and D. Even back in S1 we got hints that Villanelle wasn't happy with the assassin life that involved nice clothes and a nice flat but had no human connection: she went on a date with the ill-fated guy that accidentally died thanks to poison perfume, there was the time she shot the guy in the office building but then sat down and looked super dissatisfied afterward, Konstantin hauled her in front of the therapist (the memorable pink dress and boots outfit) because she seemed off, all the Anna stuff, etc. She got obsessed with Eve in part because she felt seen by Eve, and then they did have a connection. So I do think Villanelle, across the three seasons, has grown increasingly dissatisfied with her empty life, hit a breaking point after Eve's crushing rejection at the end of S2, and this season was looking for change that would make her happy (why she was desperate to be promoted this season, then why she wanted to go find her family). So she's looking to change her life to be happier. And she's definitely burned out on taking orders all the time--she wants to feel like she's in control, not a puppet for other people. Not a sheep. That's also why she went to find her family, to feel in control of that knowledge.
But with that all said, the show this season also strongly implied that killing her mother broke something inside her--she didn't have any problems with killing itself until she went to Russia. I do hope they delve into why that is next season, even if Villanelle eventually is able to kill again like she used to--did Villanelle think on some level that killing her mother would solve all her problems and is even unhappier now that it didn't? Is Villanelle haunted now by the fact that she will never get what she wants from her mother, so actually regrets killing her because she will never get what she was seeking? Was her mother really what she wanted to kill all along, and now that she has done it, the fire is simply extinguished, or even does every kill remind her now of killing her mother (which she regrets)? Is she unconsciously trying to tamp down on the murderous side of herself in the hopes that she can then have a normal life (the irony being that Eve had that normal life and now wants what Villanelle has grown tired of)? Super interesting stuff that I hope the show dives into.