Not much of a choice though. Mostly due to RPG females either being prone to kidnapping (which would get annoying), being prone to triggering some kind of plot based destructive surges of energy (home ownership's a bitch), being prone to dying young (granted this one would too but at least there's a Valkyrie Staff for that (provided anyone could use the damn thing)), being prone to spawning derpy kids (taken care of in this scenario), being prone to be underaged in a rather creepy way (nuff said), being prone to having traumatic pasts (hello massive psychiatric bills), being prone to be useless as hell (especially inside a kitchen, nothing like cooking that's toxic as hell), or some combination of the above.
Good point, but you're forgetting a few:
-half of them appear to have an eating disorder. 'Oh no, I weigh 100 pounds, I'm way too heavy! From now on I'll only eat apples!'
-even the independent ones don't function well in society. Not being able to bathe regularly and dressing themselves properly are common problems. For instance, most seem to be unable to dress appropriatly for something as simple as taking a walk in winter (they'll wear a bikinitop, a miniskirt with half a dozen zippers and snowboots with heels, or something like that)
Forgot about the rampant anorexia but I do feel that part of it is at least due to underagedness of depicted females and mostly due to the fact that they're based off of conservative Japanese BMIs without any consideration to the whole idea of athletic builds, body fat, or skeletons (plus it tends to afflict everybody and not just females).
Having temperate immunity does have it's advantages though along with complete immunity to filth or wear and tear even though realistically speaking, most video game female attire wouldn't last five minutes in the real world, and the same could be said of male wear as well but for different reasons (body paint alone isn't enough to save you from an indecent exposure charge and hey remember that full suit of plate mail with spikes on its spikes and that gun/sword that's as large as you are....?).
Additionally I could see the lack of potty training and healthy feminine hygiene to be an issue as well, but this is as far as I'm willing to cross that line on.
Aeolus- Well...there's this lady for you, I guess.

I'll admit it, I've never played Lunar:EB before, but given that it's a Game Arts game I can already seduce that I wouldn't like the character given that she's irrelevant to the plot either because she's mostly annoying, or gone as soon as her tenuously strained ties to the plot give depending on whether she has any significant screen time or not. So far the most likeable female protags I've seen in a GA game would have to be the protags of Walking School.
WHY ARE THERE SERIOUS ANSWERS
Frankly I'm having fun sperging out over the ridiculousness of imagining any of these 'female characters' actually trying to function in the real world. Or are you referring to somebody else?
Besides my real answer would be to make my own RPG girl, with Blackjack and
T.J. Hookers, or to say "Fuck it, I've got a life!" and get a real one (BO be dammed).