Darvond: Remembering the endless excuses they gave to avoid having to make a female protagonist, that reminds me of "Why come no girl" in Legend of Zelda where all they had to give was a shitty excuse about the "balance of the triforce".
MichaelD.965: It was doubly stupid for Ubisoft because they already had playable women in Brotherhood multi-player and Liberation. So the one time (the French Revolution) where an assassination was famously done by a woman, and they stupidly throw it away because their completely broken co-op was more important.
I could mention the Dragon Quest series. Dragon Quest 3 and 4 both have the option to make the hero female, but the Dragon Quest 5 took it away (one could argue it's due to the importance of marriage in the game's plot), and it didn't re-appear later in the series (despite the justification being gone) until DQ9, and even then for just one game (I don't count DQ10 for the same reason I don't count FF11 and FF14 as main series FF, as they're not the same type of game and should not have been given main series numbers).
It's also worth noting that, from a feminist perspective, DQ4 is far better than DQ5. In particular, just looking at the roles of female characters:
* In DQ4, we have Alena, who is a strong woman. That's true even in the literal sense, where she has the highest Strength stat of all the characters in the game (and is notable for being the only female character in the series to not get any spells or MP at all). She doesn't go alone (though she wouldn't mind doing so), but only because the developers decided she needed some magic backup for her chapter. During the course of her chapter, she, a princess, rescues both a fake princess and the princess of another kingdom.
* Also, in DQ4, we have a pair of girls who adventure off on their own to avenge their father. The only reason they end up needing help for a man is that the game isn't balanced in a way to make pure mage parties viable, and even then saifd man is considered less important by the game (if he's the only one alive, it's considered a game over).
* I could also mention that the hero can be female.
* In DQ5, on the other hand, the female characters just aren't as interesting. Young Bianca, who shares the (always male) hero's love for adventure, is the closest exception, and even she goes out with a male character and is a mage from a gameplay perspective.
* There's Bella, who is a minor character, much like that one guy I mentioned in DQ4; she's only with you for a couple dungeons, and she is not capable of leveling up.
* Flora and adult Bianca seem to have no purpose other than serving as wife choices for the main character; they really don't have their own agency. (Note that Debora was not present in the original version of the game, so she doesn't really count.)
* There's sexism when it comes to the main character's children. The protagonist and his wife have two children, one son and one daughter, but of course it's the son who gets to be the legendary hero, and the daughter isn't even that useful in battle.
(Another series that took out the female character option is the Ultima series, specifically Ultima 8 being when the option was removed, but my Ultima rants are too numerous to fit in this one post, so they will be saved for later.)