Okay first of all, your art is amazing!! I love how sharp you make him!
Second, to answer your question there are a few things I really like about him that have made him my favorite.
Aesthetically the sciencey nerd look has always called to me and the way he can switch from looking very cute and sweet to sharp and dangerous fascinates me! Even when he goes through his sage mode arc and changes up his look he still has that going for him, even though he mostly only uses the sharp/dangerous part. (tell me his little snake cloak isnt fucking adorable)
Character wise my favorites are almost always the assistant to/student of the villain and since I got really attached to Orochimaru when I watched Naruto for the first time, Kabuto naturally wormed his way into my heart. I find him to be a microcosm of how the ninja world treats its soldiers, in that his desperation for an identity and belonging allowed the forces that be to co-opt him into someone that only lives to serve them/their interests. If Danzō could have perfectly mass produced amnesiac war orphans in Kabuto's image I doubt that Root would have ever been fully dismantled and in the event of Danzō's death it would most likely have been carried on by one of these recruits (see: how kabuto reacted after loosing Orochimaru). On a more personal level I find him to be charming and funny, even though he's also an asshole, and I see that under the sharp, cunning exterior he grew in defense, there is a boy who just wanted to help the people he cared about (his mother & brother) and maybe to be cared about in return. I daydream about him a lot (I'm always daydreaming about something but for the past 5+ years he has been the main theme) and most of the time I just like to imagine how he would react to being loved, not for what he can give or provide, but for who he is as a person even if he doesn't quite know himself.
He's also very gender, which helps. I've mentioned it before but irl I've slowly been looking more and more like him lol (I have silver hair, round glasses, and a deep appreciation for sleeveless turtlenecks). It wasn't even entirely on purpose but I've given up on fighting it lmfao.
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