Pondering further, if this story is a wild, silly, fairytail space adventure where the norm is being thrown out the window, then yes, my preference would be to see the player as something other than a tween, generic nerdlike male. I get that several of the scenes are followed up with [this won't change anything even if you don't see it] but eventually that's going to run stale with it's illusion of a choice.
Well... maybe. The is always the chance story and art could be entertaining enough that even as a kinetic novel it stands on its own.
Moreover, if they did end up changed, feminized, or turned into a futa, or even started as a gal, it would be refreshing to see the changes to their bits actually matter. A lot of pretty, but otherwise middling 3d art style games have futa in name only, as the story just has them behave as a typical male harem gatherer.
Best of luck!