Short of a pituitary tumor, no boy even starts puberty until age 9 at the earliest. The problem is that the protagonist in UD(2d version) looks, talks and acts like he could be on the younger side of puberty. High schoolers don't need to sit next to their teacher to get help with math! High schoolers aren't a foot and a half shorter than their mom! A 9-10 year old boy is around 4 foot 6 on average. At 12, they're about 4 foot 10 on average. At 14, their height is nearly equal to the average adult woman. An 18 year old shorter than 4 foot 10 would technically be a "little person".
My suggestion, converting any of these 2d shota games to 3d(with literally more realistic looking models) is to shift the portrayal of the young MC to be a little bit further along in puberty, so 13-15+ rather than 9-12. Otherwise you are flirting with the elements of a CP charge, friend.
I find UD hilarious precisely because it's so ludicrous, but if you made the imagery more realistic(i.e., 3D), it would shift to being way too creepy unless the kid was portrayed as significantly older.