As for Ugly well-liked females in gaming.
Ellie - from Borderlands
Milliena - Mortal Kombat
Sheeva - also Mortal Kombat
Birdo - Super Mario Series
Tali - Mass Effect (mostly cuz you never see her and she only has three fingers)
Freya - Final Fantasy 9
Moira - Fallout 3
Karrigan - StarCraft (post zergification)
Kassandra (Assassin's Creed: Odyssey, personal taste of mine but I didn't find her attractive and she is loved)
Well, guess I should give my own two cents about these. Birdo and Freya aren't human (or very close to human in that green-skinned space babe way). Don't think conventionally (un)attractive standards apply to them. I agree with Ellie (tho there's people into BBW, but that's of course an outlier) and Moira. Tho in Moira's defense, creating good looks in that game's character creator is really fucking hard and everyone in it looks gonky (without mods). Sheeva is borderline, I guess. Guess that depends if you're into Grace Jones (cuz let's face it, Sheeva is Grace Jones with extra arms). Which leaves:
Mileena: The hotter and more dangerous version of Kitana, who already invokes the sexy ninja trope. Basically an attractive swimsuit model/pornstar, with one monstruous bit slapped on which is hidden most of the time, probably to not distract too much from how sexy the rest of her is, and usually comes dressed in some of the most stripperific outfits out of the entire cast.
Kerrigan: Another Hollywood attractive woman with a swimsuit model body with monster bits stuck on. More of them this time, but also in such as way that doesn't cover up the pretty face and nice body. The opposite in some ways even, like how it gives her smokey eyes, lipstick, high heels, and on her torso what looks like one of those bdsm corsets that leave the boobs out.
Tali: Has the same swimsuit model body every other Human, Asari and Quarian woman has in this series. Ok no, Quarians are a little smaller and more waifish. Clad in skintight suit. Not sure if it's every explained why in-universe, seems rather unnecessary for a sealed suit save for maybe saving on material, but considering all female armors/suits in this setting is rather curve-hugging, I'm guessing the out-of-universe reason is increased sex appeal. I'll admit, not as blatant about it as Mileena or Kerrigan.
Kassandra: Not that familiar with this one, but looking at art and screens, yeah, good-looking lass, especially considering she's a mercenary in ancient times. I mean, her face is astoundingly unblemished for someone with no access to modern skincare and make-up. Maybe not everyone's thing, but not what I'd call ugly. Not even plain (tho you've already pointed out its a personal taste thing, which ... fair enough)
In short, while tastes of course differ, I strongly disagree that these characters were designed to be ugly, or even just unattractive.