I enjoy deep character customization. However, with my own work, when people across the gaming spectrum gave me the same feed back, I changed it. Hopefully, for the better.
Go with what makes sense for your story, but unless you weave narrative into the customization process, it can get boring sometimes for a reader.
I like having tons of customization options. Having them used in game is even better…Liconis story does a very good job with it.
That being said, it can get tedious the third or fourth time you’re playing. I think I’m actually going to code in a quick start option myself, for Citadel. Not sure why I hadn’t thought of it, but it’s a really good idea.
Same, I never actually thought about doing a quickstart but I know for my Dragon Racer game, it can be a bit annoying if you’ve played it a couple of times after.
I’m a little bit ambivalent on it.
High costumization manages to create a much more personal feeling of connection between a character and its reader (allegedly). Players also get the chance to make their character who they want the character to be, down to the smallest details.
I think, though, that customization is better left in small quantities. Like being able to name a few characters, or pick one or two physical characteristics. I don’t really like when the author pushes, say, a bunch of clothes and gives me the choice of what my character is wearing. The choices are often plentiful, but I don’t think an author can accurately capture the type of MC I have in mind, and not the MC in all the reader’s minds.
Just out of curiosity, what about if it’s a superhero game? Like your costume choices on Hero Rise?
When the choice has meaning, like in @malinryden’s “Fallen Hero” and it actually matters - her use of the uniform customization is a great inspiration.
In heroes rise The uniform doesn’t do anything except a minor stat stuff so I don’t really care. I would care if changes some minor stuff as How people reacts to you in some flavor moments.
Customization for the sake of it with no doing anything and not being saying about it. In my book is stupid and unnecessary. I just pick those random. No sense for me.
Well I never like the option to customise npcs, maybe customising your family as in if you have a sister or a brother would be ok, but nothing too much. Maybe change their appearance based on the mc’s appearance. But yeah, as it’s been said a choice needs to matter, my personal pet peev is when gender is just flavour text 
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I think in an interactive novel no customisation should be implemented though. But in a true CYOA game as much as possible is good to make it more personal, but I think big customisation options like height aren’t good tbh. Like if you take two mc’s one who is say 4ft12 in and one who is 7ft, every npc will surely have a different reaction, so to right different reactions for every single npc based on that, plus any additional customisation options such as eye colour, hair colour etc is just too ambitious as it’d be too time consuming to implement convincingly I think. So manageable things like eye colour, hair colour etc are good as the difference in reaction shouldn’t be too different and not with every npc I don’t think? 
plus you could just focus on more depth to fewer options, E.G one mc might be really self conscious of a scar, another not so much etc.
There are actually guidelines that gender shouldn’t be a negative or positive thing. You can find the guidelines here.
That’s why it sometimes feels like our genders are only flavor text. There’s a WIP, Broken Lenses, that has some changes based on whether you’re male or female, but even then, it’s only really flavor text. EDIT: Okay I worded this really poorly. I meant to point out that this WIP tries to make gender actually have an impact on gameplay, as you want, but (as of my last playing) it had stayed mostly flavor text…particularly because it’s difficult to make differences in gameplay without making one seem better (against guidelines) or seeming pedantic. I have since been informed that further changes have been made. @Interestedparty, once again, I’m super sorry for wording it in a way that was hurtful! :C
Just thought you might find that information interesting. 
So basically try to get as close to equality as possible?
In my game gender is important in several different ways. Not for discrimination only. But like in real life gender identity is important. There is a ball of coming age where each women is forced to go with a complete Victorian corset dressing and additional stuff. Male could dress everything except the Victorian dress. And that could lead to character complaint or not say they want to wear the dress being male or a lot of situations like a duel to first blood against a Girl who dare insult Victoria and corsets…
I mean that’s what I feel important in customization It has to impact and change something even If only a small scenario. If not I don’t care. I don’t let you choose heigh or apparence because it won’t affect anything at all. If I let you choose something is because it would affect game
Oh, as someone who once played with the idea of a Superhero WiP, the question has crossed my mind.
And I think it’s best to just let it slide and not make it a choice, because, as I said, it’d make it harder to make it fit into the reader’s idea of what their hero is.
It’s an example I use a lot, but… it’s kind of like how the Infinity series never suggests what your charcater’s skin tone is, and how they’re supposed to look like. You have absolute freedom to decide.