Noob is #3. The amount of people that requested him definitely surpasses Reptile at this point. Rain, Ermac, and Smoke are generally requested, too, but probably not as much as Noob.
I think Reptile lost a lot of steam as a character from MK4 onward. I love his reptilian design moreso than the original humanoid masked appearance (Excluding MK4 and MKDA...those were pretty wack). But the humanoid design was iconic and, though the change was largely an attempt to capitalize on advancing technology and less memory constraints, MK4 and MKDA's redesign of the look of Reptile left a sour taste in fans' mouths. That, and his story never really goes anywhere meaningful, sticking him to jobber roles. I actually think he may be bottom 2 in popularity amongst the male ninjas, sharing that placement with Chameleon.