Do you think it's the kind of thing that'd be improved by an upcoming patch, or would it get better only when a Definitive Edition gets released, if at all?
I think it's the sort of thing that will take steady patching over months to fully straighten out, but it's not so extreme it'd normally need a Definitive Edition.
To be clear it doesn't make it unplayable - the quests seem to stage correctly in the underlying game. It's just that the journal becomes increasingly less useful.
I should note we haven't seen any serious patches yet, just an assortment of hotfixes, all of which have contained a lot of fixes but not actual improvements (nor balance changes, though that's probably for the best for now), and this would probably largely fall under "improvements" rather than just fixes.
Karlach likely falls into the same camp--too much connection to powerful dark forces and possible "that's who I want to romance" rather than "that's who I want to be."
Karlach is the second-most-popular origin on the chart, so I think it's only "that's who I want to romance" holding her back at all if anything.
Wyll it is going to be a combo of three factors I think - first off, in EA, he was more boringly written than all the other characters. His dark secret was seemingly just that he was a Warlock, which is not much of a fun dark secret compared to everyone else. And yes, he's kind of naughty word-up looking. I think they were going for rakish but the stone eye consistently comes across as creepy, but he doesn't have a personality that leans in to creepy.
Stereotypical Main Character syndrome.
Beyond being a white man, he doesn't fit that at all though.
He speaks like Richard Ayoade's character Moss from the IT Crowd, rather than in a commanding way. He has mucho hair, and it's fancy. He's not physical/strong/pushy (despite his character model being hilariously ripped, because they all are). He has no military background, even in the past. He's a Nice Guy (TM) of the worst kind personality-wise, rather than a Bad Boy or just attractive/charismatic.
So I think we have to rule out Stereotypical Main Character in his case - if anything he's slightly closer to Type 2 Main Character, the Spider-Man/Jedi Survivor-type. But he is a white male human, and that's the real thing pushing him into the lead origin-character-wise, I would personally suggest.
Astarion I think you're right on - he's even further from the stereotype and is that kind of fancy foppish Brit who Americans are confused by and think has to be gay (the vast majority of people who talk like that are straight though). But he's still extremely close to Karlach in popularity because he's a vampire and funny as naughty word.
Over 93% rolled custom characters? Well, may that will put to bed the belief that origin characters are better (but, given that this is Larian’s second game with them, probably not).
I mean, popularity has never reflected whether something is "better". And we had Swen himself saying "Play a custom character first before the origin characters".