Interesting read; it's often something I've thought about myself.
I think making identifiable leads is something that can be addressed incrementally. Right now, just seeing more female leads would be nice. (Especially since studies of Tomb Raider show that a lot of male gamers like playing Lara Croft, even if for no other reason, they like looking at her rather than some beefcakey ass running around. I think this--and the other reasons for male players being fine with female leads--can extend easily to other games.)
Likewise, more variety in appearance/race would be nice. I don't think those things in itself require a whole lot of re-thinking/extra technology.
The complication comes in when yes, you have romance or sex interests.
There's option 1: don't have romances. Most video game "romances" I've played through suck anyway--I feel like I'm romancing cardboard. (The only one I ever enjoyed was TNO and Annah in Torment, and that only went so far--but it was extremely well written.) I'd honestly rather have no romance then have, say, some guy I've tried to ignore the entire game suddenly throws himself at me because the game's script told him to (I'm looking at you, NWN2).
The fact is, beyond sexuality, it's nearly impossible to design a love interest that appeals to everyone. We all have different tastes, and what one person finds hot another person is going to be disgusted with.
Option 2 is what Bioware does: be reasonable, give the player the choice of gender and race (this to me is always my favorite solution to the lead-diversity issue), and design the romantic interest from the perspective of the NPC--if you're female and they're a straight male they'll hit on you, but so will the gay female on the team. The straight female will not hit on you, however. They seem to be already capable of creating a set cast with well-developed NPCs who can at least appeal to several if not all gamers, so if they just keep doing what they're doing and build on it as they're capable, there will be a good system.
Also, importantly, you should ALWAYS have the option of turning down a romance or sexual offer. If you don't have the resources to program in a romantic partner for every potential player, someone who's turned off by the offer should be able to turn the character down--and with a better dialogue option than something that makes your main character sound like a douche. (I remember in Baldur's Gate 2 "leading on" Jaheira because any choice I had to get her to stop trying to romance me was something like, "Shut up you stupid half-elf *****" while apparently something like, "Uh-huh, that's nice," was a major turn on to her.)
Some day devs may have the time and money to program in multiple leads and multiple romance interests and I think it may actually be possible one day. In the meantime it's still important to do what you can to be as inclusive as possible, even if all that is is being able to toggle the "male/female" switch in the character creation screen.
For games like Overlord, any "relationships" therein are purely shallow and sexual, with no real personalities to worry about writing (I haven't played Overlord, so correct me if I'm wrong). Seems easy enough to make some beefcake meshes and slap them over the harem, and let the player choose what kind of member of the harem they want (in fact, when its time for you to "earn" your next harem member, let them choose from a list--you can therefore get the ones you want, both male and female of a variety of appearances). Seems well within today's technology, and all it takes is a couple more character designs and animations and you're done.
In addressing Shamus's questions at the end: "Does this sort of thing keep the ladies from playing? Do females stay away because games are made for men, or are games made for men because females stay away?"
As a female gamer, I've noticed many games I play are assumed to be "made for men"--despite the fact that research shows that 40% of gamers are women. So if I were to stay away because games are "made for men" I wouldn't have anything to play.
I do stay away from games that appear to be particularly degrading to women. A little cheesecake is fine (as is beefcake) but if every female character is there simply to be fucked or slapped around.... or even to just be weak and useless... I'm not going to play it. I know that kind of thing is going to lead to me feeling angry and attacked personally, so I'm going to avoid it. It's why I avoided The Witcher despite being an avid RPG fan; people kept saying it was the best RPG EVAR, but I kept reading the nonsense about seducing women for rewards and it just didn't sit right with me, so I kept far away from it.
But I won't avoid a game just because it has a male lead. My favorite game ever is Planescape: Torment which has a male lead--and a fantastic story. I'm bi so I'm happy with the romance, and you can avoid the romance easily enough if that isn't your thing. The story is excellent and all the characters relatable to in some way, so the fact that the main character happens to be a guy isn't a big deal to me.
Likewise, I--like a lot of female gamers--like to play JPRGs, which are almost solely dominated by stories with male leads (usually annoying, bratty, teen male leads at that). I can play games like that, even if I can't identify with the lead, because there are still other great characters, male and female and other, to enjoy. One of my favorite series is Suikoden, which has a lot of strong women to relate to and characters of all stripes, shapes, colors, and sizes to enjoy--truly something for everyone. I think the JRPG genre in general does inclusivity pretty well. And I think FFXIII's having a female lead is a nod to the fact that so many players of JRPGs are increasingly female.
Wow, that was a teal dear. Sorry about that.