In my opinion, I do believe Klein, the Shnee family butler, is Neo's father. He's old enough to have a child or two, and she's quite young, after all.
For starters, let's look at biological, local, and behavioral similarities. Most importantly, both of them can control the color of their eyes, a trait no other characters have yet exhibited, and Monty, Kerry, and Miles have all said that a character's eye color is VERY important. Furthermore, they both have fairly short statures, with Klein looking to be on the shorter end of the spectrum of adult male characters, and Neo being the shortest character in the entire show. In addition, even with the makeup that goes with her "Gentry" theme, it would make sense that Neo is pale if she comes from Atlas, being as it is a cold area, where smokestacks can blot out the sun for miles. And how about their attitude? Klein is clearly a jovial fellow, and enjoys spreading smiles. He seems to take the "fun uncle" role, able to put a smile on sad situations. Neo is also quite enjoyable, only breaking her smile twice so far, once when facing Raven, and the other when being flung off the airship. Like Klein, she clearly takes great pride and joy in her work, depressing as it can be.
But how about those powers? Well, the World of Remnant series tells us that there was once an ancient practice of people infusing Dust into themselves. This gave them incredible power, using the abilities of dust to it's maximum, but fractured the infuser's mind, and often left them crippled in some way. Great power? She can teleport, create after-images of herself and those nearby, and disguise herself in just about any costume, even changing her hair on a dime, so check. Mentally unstable? Yes, she's showed signs incredible sadism, and looked up to Torchwick like a father, genuinely idolizing him. Crippled? She can tell you all about that... oh wait. Check. Now, where could someone find a massive supply of Dust, enough to infuse to the breaking point? Atlas seems like a good place for that. And would it not make sense that the butler to the family running the world's largest Dust producer would receive some Dust themselves, as pay, bonuses, gifts, or samples?
EDIT: Also, Klein is German for "Small". This is a trait very commonly associated with Neo.