Adrian Andrews, a central character to the final case of Phoenix Wright: Ace Attorney: Justice for All and had a minor appearance in the 2nd case of the 3rd game, Trials and Tribulations, is far more popular in the fandom than any other side character. This partly has to do with her having the central role in a fan-favorite case, but more importantly, there's the implied Les Yay between her and the Whip It GoodTsundere Prosecutor Franziska von Karma. This might also be because fairly early in the case, she turned from being a hard-edged talent agent into a soft-hearted puppy, because she was the real victim all along. Some of that may also be explained by players feeling guilty for having to re-accuse her of a crime they know she's innocent of to bide time, and later being forced to choose between her life or Maya's. It's quite a feat to have the player feel personally involved like that.
Before Adrian Andrews, there was Phoenix's rival, Miles Edgeworth. He even got his own game!
Games. You know you've succeeded when your new series puts out a sequel before the old series can even get a new game into the development stages.
Until Apollo Justice hit the market in America, Ema Skye appeared in all of one case (albeit a big one) in the first game as a stand-in for Phoenix's assistant, Maya. However, she apparently struck a chord with people, given that her coverage practically eclipsed Maya for a while — maybe it was the magenta goggles and flair for scientific investigation. She was almost the protagonist of Investigations before a certain cravatted prosecutor took over.
Don't forget Matt Engarde, who only appeared in ONE case, but has a huge fanbase. His rival, Juan Corrida, was just the victim of the case, and he has gained loads of fans (though this may be because of fanartist Zarla's works).
Byrne Faraday of Ace Attorney Investigations has also become very popular, despite the fact that we see exactly one screenshot of him before finding his corpse. Probably has something to do with being a good father to Kay, a master thief, and one of the very few prosecutors who isn't an Amoral Attorney.
Don't forget Gumshoe, pal!
Also, Maya Fey. Trucy was criticised simply for not being her.
Detective '''Badd'''ass in Investigations. You know you're popular when you're the Ace Attorney equivalent to Chuck Norris.
The release of Unlimited Blade Works, however, may also put Lancer in this position. Sfter the release, a lot of message boards (those who played UBW) were saying "Lancer is more GAR than Archer!" And yes, he's never alive by the end of any scenarios like Archer.
Rider as well. It's too bad she gets so little screen time even in the route focusing on her and Sakura as the heroines.
Playable Caster of Fate/EXTRA likely qualifies. She's barely promoted at all, but she's only a little behind Saber in terms of popularity in Japan, and probably surpasses her by a large margin in the west.
To a more minor degree, Assassin. Many people find his calmness and his katana and the way he was able to stand up to Saber despite his limitations far more awesome than any of the above. And then, of course, there's the music that plays during his fight with Saber in the Fate route.
Yuki for numerous reasons. The main reason is that he's the nice guy to Makoto's jerkass personality and probably the only sane man that is genre savvy enough to realize what's going on. He can call Sekai out on everything she's done to Kotohana and punch Makoto for being a dick. Finally he's the cross dresser that many guys have deemed more attractive than the girls of this series.
Higurashi: When They Cry: Rena may be the most iconic character, the most commonly related to the series, and her popularity may dwarf the true protagonists', but she's truly relevant in only two chapters. Still, the creator seems to have taken this in stride; see Wolverine Publicity.
To be honest, she's a pretty crucial role in almost all the arcs/chapters. She's also the mascot of the series.
Not to mention that the arc where she is the central character is the turning point of the series.
If you're talking about Rika as the main character than Rika is pretty damn popular too. If you're talking about Keiichi then its to be expected, he's not a female character after all.
Black Battler; despite being an illusion created by Bernkastel, he's gotten popular enough to join the roster of the fighting games.
For the fans of Tsukihime, Nrvnqsr "Nero" Chaos and Satsuki "Sacchin" Yumizuka seem to be well liked, with the former due to his badassness and the later for her cuteness and unfortunate fate both in-game and metawise.
Sola seems pretty popular with the Sunrider fanbase, despite not having appeared in the game proper.