I've never really picked up on Hilda being that popular, usually the most popular female MCs I've seen have been May, Dawn, Rosa, and Serena. BW1 itself has been popular but I haven't really seen a lot of hype for its protagonists aside from "OMG they're older".
Really though, I don't care about who gets alts as long as the type diversity is covered. Issues such as the lack of a Johto Electric sync pair until Kris & Jolteon matter to me much more than seeing Kris get a sufficient amount of alts.
It's hard to say how popular they are against the rest of the franchise as they haven't done any mass polls for the characters like they do the Pokemon. The only polls we really get for the protagonists are the Nintendo Dream polls or the like where they're against the rest of the characters of their region, and in that case they did pretty well with both scoring in the Top 10 behind the obvious suspects like N, Elesa, and the Subway Twins. Interestingly enough, in that poll Hilbert was more popular than Hilda, which is probably why he got an alt first before she did.
Anecdotally, Hilbert to his credit tends to be one of the more liked male protagonists from what I've seen, generally being behind Red, Ethan, and maybe Brendan whenever the topic pops up. Hilda is also pretty liked, but I'd put her behind at least May, Dawn, Serena, Rosa and maybe Gloria, with Rosa surpassing her thanks to Masters putting her in the spotlight.
I would like to see an official poll one day for Pokemon characters to see how the protagonists would fare, but characters have generally not had as much pull as the Pokemon so I doubt they'd ever do anything akin to the PotY poll for them.
Why do they like that Hilda so much? Such a bland looking character that didn’t even appear in the anime
Even Serena and Dawn got less alts than her.
Ignoring bias, Serena's going to tie Hilda once the Kalos VA drops in a couple months and I wouldn't be surprised if Dawn gets a seasonal very soon as well. It's also not like Hilda's beating them by huge numbers as she's only ahead by one, and Serena also has a Master Fair over her so it's clear that they place a lot of value on her regardless.