I don't recall this dialogue, but I'll grant you the point. This could yet be a stepfather (known to her or otherwise), but I'll agree it tends to argue against MC being her father.
I think it would have to be here, though, because the issue is whether MC is the biological father of any or all of the 2019 girls. He wouldn't be, or become, their stepfather, and his doing so wouldn't cause any kind of time-travel paradox.
We see two "ninjas:" the "shit-ninja" who threw shit at Shelby, and the ninja who helped MC and 2019-Darci free Gabby. The latter is shown to be Darci, and I believe she looks considerably older than 2019-Darci. I don't think we're given any reason to believe, or at least to confirm, that the two ninjas are the same person. The shit-ninja is widely believed, based on comments in this thread, to be Darci, but that isn't confirmed--though Darci's martial arts skill does suggest a connection there.
On the time travel thing, I think it's reasonable to suspect that it's possible to travel in increments of other than exactly 20 years, but we haven't yet seen (clearly), or heard of, that happening. April? 20 years, forward to 2019 and back. MC? 20 years, back to 1999 and forward. Darci? Well, we don't know, but it kind of looks like she did--we don't know exactly when the ninja Darci we saw in 1999 came from, but it appears to have been from after 2019, because she looks notably older than 2019 Darci. Though that could have been 2039 Darci coming back to 2019, and then to 1999, I guess.
I still think, with what we've seen so far, MC being Skylar's father is more likely than his being anyone else's father. In order for him to be Skylar's father, we'd yet need to see that:
- He has sex with 1999 Luna (which I consider all but certain), and
- The person that Skylar refers to as her father is not in fact her father--perhaps (most likely, IMO) her stepfather, possibly some other friend or family member who served as a father figure. In the case of her stepfather, she may not have known better. This strikes me as pretty plausible, but that isn't with a great deal of thought.
- MC needs to go back to 2000-2001 and have sex with Scarlett/Khloe again
- This could be that he waits until 2020-2021 and travels again, or that he's able to travel 18-19 years rather than the 20 years we've seen thus far
- I'd think this could be kind of hard to explain to 2000-2001 Scarlett/Khloe, but porn logic certainly applies
- But there needs to be some reason for him to go back to that time; I don't think the old man's going to send him back for a booty call.
And I still haven't heard an explanation for 2019 Luna's reaction to meeting MC (she completely freaks out and forbids Skylar to see him) that makes more sense than that he's really Skylar's father. And if Skylar's been told that someone else is her father, all the more reason for this reaction.
All of this is speculation--as you say, we don't have all the information. We'll no doubt get more as the game proceeds, but we'll probably be left guessing on some of these points even once it's over. But it's kind of fun to speculate.
