I can't think of any overtly ugly main cast/party member female characters that aren't villains (ie not an old hag/witch), but I know some that aren't particularly attractive. April Ryan, the lead character of The Longest Journey. Annah and Fall from Grace (she breaks many succubus stereotypes, and is quite a far cry from those of other RPGs, such as World of Warcraft, Disgaea or the Darkstalkers fighting games) from Planescape: Torment, both of which are party members. Though those two are the best written adventure game and best written RPG of all time respectively, so that is to be expected. Oh and then there's Alice from American McGee's Alice and Alice: Madness Returns. Then there's Chie and Naoto of Persona 4 (and there are more "normal looking", non eyecandy female characters in the Shin Megami Tensei&Persona-series games). There are more such characters in other point&click adventures and RPGs that I can't remember at the moment or haven't played, but these are just some of the more memorable/prominent female characters that I can think of at the moment.
Generally it's a problem with writing. Nintendo games and AAA titles don't bother with that shit. Find a game that focuses on writing and intresting characters like Longest Journey, and you'll find female characters that aren't just eyecandy.
None of these are really hideous, especially Persona characters are all stylish and sleek. But all of them (with the exception of Alice, it's an action platformer so it doesn't have a deep story) have personality and character and aren't just useless sex objects.