This is one of those topics that I'm a little loathe to get involved in, simply due to the entrenched positions and arguments that result, but I would like to add some information that I am qualified to do:
I am a dev for a studio in Scotland, a proper one. Not someone dabbling in Unity or thinking about maybe, possibly, signing up for a coding course. I write games. I am a programmer and work closely with artists and animators, although I sadly display no signs of artistic creativity and would never be able to do what they do.
Tim Schafer was being a little disingenuous with his (admittedly cute) gif showing a gender-neutral base character adorned with a different hairstyle and clothes. If your art style is this simplistic then, yes, it is a trivial task to have both a male and female protaganist for very little additional effort.
If, however, you are cooking up a latest-gen game for PC or console, then we are at the point when you absolutely have to employ mo-cap to get the animations right. Whilst it is a simple task to substitute a female character mesh over the skeleton of your male character and re-use the animations I can assure you that the end result just looks... wrong. I can't honestly put my finger on why this is the case and, as I previously mentioned I am not an animator, but it's the Uncanny Valley of animation. Males and females walk differently - the differences are tiny and subtle but we're good enough at spotting unexpected patterns to be able to see it looks odd without being able to identify precisely where it's not working.
Result: Two actors needed for mo-cap studio for all animations. Twice the cost, twice the time.
Everyone expects voice and lip-synching in animation, regardless of the game genre. Although we have tools that automate a lot of the synching, much of it needs to be adjusted by hand and there is no way two voice actors are going to deliver the same lines in some kind of Pacific Rim synchronisation. Can't be done.
Result: Two voice actors and twice the amount of time required to perform synching and tweaks.
If you are going to include both genders as your lead character then, as someone pointed out previously, it has to be a design decision at the start of the project. NPC dialogue needs to be gender neutral, unless you have the resources to do two sets of said dialogue and, if you do this, you'll then need two sets of localisation text for subtitles for each language you localise in.
Result: Agghhhh.
I could go on, but I'm sure you get the point and this is going to be a wall of text as it is.
Now...
The thing is, it has been done and done successfully. Mass Effect and Skyrim spring to mind, pretty much every MMO I've played, and they also had to add additional clothing/armour meshes for each gender but they put the work in. I wonder if the Bioware team thought the effort was worth it though:
ME1 - 18% of players played FemShep - http://www.eurogamer.net/articles/2011-07-20-bioware-18-percent-play-mass-effect-as-femshep
ME3 - by the third installment, this number had gone up to a staggering 20% - http://www.pcgamer.com/2013/03/25/mass-effect-3-infographic/
I would say it is worth it. AAA studios really have no reason for developing single-sex protagonists unless it is an integral part of the story. I'm struggling to think of a game where this would be the case.. perhaps something like LA Noir is a suitable example, but they're rare. However, the lame-ass excuses from Ubi are essentially invalid because what I've mentioned above would only add a small percentage to the overall development costs. They should have done it, even if just for that 20% of players, because that number will grow and grow and grow; if you get a set of people on your side, that is banking up goodwill and future sales.
If your fave indie game only has a male or female character, perhaps you now understand a little better why this is the case. I suspect my friends over at Rockstar North are breathing a sigh of relief that no one ever fired this complaint across the bows of their GTA titles... imagine how much fun it would be to have a female sociopathic bad-ass and the dialogue that could go with it... The buggers can afford to do it, too!
Missed opportunities everywhere.