|Question, how can we be certain Jonas didn't clone Rusty? We've seen that Rusty copies much of his fathers work, so the cloning had to be near completion if not already completed. So whose to say Jonas didn't clone Rusty without anyone knowing?|
Yup, my thoughts exactly. Sure, maybe Rusty finally invented something for once... or maybe he just re-used (or built up) something of his father's again. Meanwhile, the "purgatory" computers from the cloning facility are from Jonas's era.
We've only had the slightest glimpse into the life that Rust had as a kid, and slowly and surely we're seeing a dark side to Jonas's private life. We've seen that he made mistakes and amoral choices (MOM computer, and abandoning kids under the complex), and apparently slept with hookers or whatever. Walked around with his junk hanging out at the breakfast table. Took his son on deadly missions. His body-guards played deadly games with Rusy to man-him-up.
Between the slow reveal of the man's private life... I wouldn't doubt that he had to clone Rusty a few-times on the down-low to keep up the public image.
It could also explain the whole Rusty Jr situation, which the whole twin-absorbing-the-other in utero isn't unheard of... their "unique" situation could be explained by "super science" instead of some unrealistic plot hole.