Yeah I played KOTOR 2, but it was a long while ago. I played as the male, and only learned years later (~2013 or so), that it was intended that Revan was a female.
When playing a game, it the developers come out later (or even before release) and say, "Hey, this was the canonized version", that doesn't actually help unless the people playing the game actually hear about it. I was also 14 at the time, so for all I know, they could've had a huge marketing campaign informing gamers that the female choice and I probably would've missed it. But hey, if any relevant information is in the game itself, I'd probably see it.
But I won't play through the game a second time if there's no difference (and even then, the difference has to be worth playing a second time for), and if I don't know there even is a difference unless I play through it twice, it becomes almost a chicken-and-egg problem. The only solution is if I accidentally stumble across information on the internet (before I even start playing it), or if the game itself provides the information during the choice-making process.
This could be done by making the female character the default-selected one, saying "(Canon)", and the male character saying "Alternate version", if it's plot related.
But if it's not plot-related, and developers actually want players to replay the game a second time, this can be encouraged by, when development budgets permit, giving significant enough differences to their stories and the areas they reach (imagine if each had even a single unique planet they visited - that'd be worth a replay), or their abilities, that it makes a real difference and of value to replay.
Basically I have three preferred options:
A) Create the character and stick to it - either design around a female protagonist or a male protagonist, and don't give players a choice (I'm fine with this, even with female protagonists!). Mario, Link (in Zelda), and Masterchief are always male. Joanna Dark and and Samus Aran are always females (though Samus is a bad example). If this is the route a game is going, I'd like a few more well-designed female protagonists. (I don't game as much as I used to, so I might be outdated here - maybe there are more female protagonists that I expect)
B) Make there be no "cannon" character, like Morrowind, where the choice doesn't matter. In which case, I'll always play the male, and no harm done to anyone (the stories usually suffer slightly for that, so a story focused game might prefer (A) instead).
Or C) Make each choice basically be separate games - each character explores different areas (with overlap), and/or has different stories (with overlap), and/or has different abilities.
I understand for "epic" storyline-focused games that last one is less likely to occur, but in those situations, if you want to tell a story, and you also insist in giving a gender (or race) choice, and one choice is more "cannon" than the other(s), then do me a favor as a gamer, and inform me of it!
You can do so in text on the selection screen, but you can also use psychological tricks!
- Make the "canon" choice look cooler. Or make that choice have more eye-catching and appealing colors. (this is more subjective - different players would have different tastes, but you can try stuff like making the non-canon choices look bored on their facial expression on the gender selection screen, and maybe players will subconsciously choose the more 'interesting' one).
- Try making the alternate non-canon choice slightly desaturated, and the canon choice sharper.
- Make the "canon" choice the default, requiring the player to take action to select another option (KOTOR 2 might've done that, I'm not sure). On its own this isn't enough.
- Since eyeballs start in the upper-left corner, make the left character the canon choice.
- Since players are more likely (supposedly) to go down a lighted hallway than an unlighted hallway in-game, they might also be more likely to choose a brightly-lit character over a less-brightly lit character. Test that during development. Use a spotlight to select a character. When the spotlight is over the canon character, make the spotlight slightly brighter (subtly so). When the spotlight is off of the canon choice, make sure she is still visible (not in darkness), and maybe have something tiny clipped to her suit or whatever, that glows in the dark or is lit up, so it catches the eye even when that character isn't selected. Additionally, make the non-canon character much more heavily in darkness when not selected, with nothing eye-catching.
- Often on selection screens, characters move around slightly, shifting their weight around. When not selected, the non-canon characters shouldn't move. But when not selected, the canon character should still move.
- Make the "canon" choice scaled slightly larger, so she/he is a few inches taller. See if that affects players subconsciously.
Do some AB testing to see if any of that actually affects anything!
All this is to solve the real problem: You have the "real protagonist", who's a female, but lack the guts to (or are pressured by non-design interests to not) make her the sole protagonist. The real solution is to not give a choice, and focus on the one female protagonist (or the one male protagonist), or to make the choice actually not matter, so then you don't need to encourage any specific choice. But, failing that, you can try to use the psychological tricks (and outright informing the player ) that one choice is preferred.
Definitely don't make the two characters look like clones of each other (in this case, by their clothing), or I'll think their storylines are clones and the choice doesn't matter.
If the female one is the canon, don't name the female selection "Female <classname>" while the male is just named "<classname>". Make the non-canon choice have the qualified name. Even better is making the choice text read, "I want to play game how the designers intended (female protagonist)" vs "I want to play the alternate story (male protagonist)".
What I wouldn't like is if the choice does matter, but it's presented in-game as if it doesn't.
Or if the choice isn't supposed to matter, but one side of the choice had more effort invested into it.