So why were Tet became so interested in Julia to the point of insisting Jack bring her to the station?
It's likely that the Tet realized long ago that Jack and Vika are NOT an effective team; she cloned them because they were the only ones she had access to.
It's unclear if Vika's clones participated in invading the Earth, but Jack being a trained soldier and a public hero would have more shock value in a Psychological Warfare against mankind.
Vika obviously had no combat abilities and was more useful as Mission Control.
The Tet probably realized that, while Jack and Vika could work together, Vika was not so good at keeping Jack on track. In fact, her behavior made him more unpredictable, as hinted by Jack meeting one of Vika's clones.
Each pair of clones has the same relationship problems: Vika being too professional, by-the-books and controlling, making Jack feel uncomfortable and restless
It's likely Tet had problems with other clones going out of control in the past as hinted at by the "are you an effective team?" question. It's likely a repeat test of Tet to evaluate whether each clone pair is still under control or not. This implies there were problems with the clone teams before, which would cause this protocol to be put in place.
Julia, however, is Jack's wife; he had dreams with her, and quickly and willingly goes out of his way to help her. If the Tet managed to get Julie, and cloned her instead of Vika, they could make what would likely be the perfect team to continue controlling Earth.
After all, Julia would make Jack (1) feel more at home, and (2) less likely to question orders Jack even uses this excuse to convince Tet that he's surrendering: "We're more effective team".
As for why the Tet didn't just try cloning another human woman before, it's likely that, because Jack's clones would always keep dreaming about Julia, any other female clones would have the same problem.
This would go double if the female clone had no connection to Jack. At least on Vika's end, it's implied that Vika was already infatuated with Jack, which made it easier for the Tet to make her Jack's wife. Since she had that infatuation, she didn't question her reality.
With Julia already having the connection as his wife, and with her being completely in love with her, the clones would be a perfect match.
Jack is shown to be a pretty competent, intuitive and instinctual pilot, especially for a repairman. One of his first establishing moments is that "backflip dive" maneuver he does with the Bubble Ship off the tower. Why would a repairman gain such skill to have no problem taking risks just flitting back and forth? He's a NASA commander. He was an elite pilot all along.
At face value, the initial story makes no sense. Earth got destroyed by a massive all-out nuclear war combined with environmental destruction, and yet humanity somehow managed to build and launch a gigantic space station and is now on its way to colonize/terraform Titan, all that using 2017 technology, no less (although admittedly their 2017 is different than ours). If they still have all these resources, can't they just restore Earth? It doesn't even look that bad! It all makes sense when it's explained that humans never made the Tet and have no plans to actually reach Titan; in fact, "humanity" is down to a few scrappy survivors and an army of brainwashed clones.
At first, Julia's strange behaviour around Jack and Vika could be ostensibly attributed to having just woken up from delta sleep. When you know the context that Julia is working with at that point in time (Jack and Julia are married, and Jack, Vika and Julia were all in delta sleep on the same mission to Titan 60 years ago, with Vika and Jack being woken early to investigate the Tet), the scene is instantly a disorienting nightmare, with Jack and Vika apparently together, with no recollection of Julia, and speaking familiarly of the alien thingo they were sent to investigate. To top it all off, the Tet is now orbiting Earth instead of being nearly 40 days space travel away from Earth, and the Earth itself is a wasteland. Anyone would react strangely in such a situation.
The alien threat hasn't actually been dealt with. The 'Tet' was part of an energy-collection mission (backed up by the fact we see no aliens - everything is remotely automated). What are the aliens going to do when they realize their power plant has been blown up?
Debatable. Based on available evidence in the movie, the only alien is the Tet; it uses an army of drones and support machines, but it's the only actual, conscious entity.
What happens to all the other Jacks and Victorias, who still believe the lie and have no idea what's happening now that the Tet's been destroyed?
If they did find out the truth, as well as about the other clones, how did those Jack take the fact that another version of themselves has settled down with Julia? Conversely, if the other Victoria's also entered into a relationship with Jack, how do they react to the news and being spurned?
The Jacks might have to see Julia to trigger any major memory recovery, and she is fairly isolated in the cabin. Also, any other Jacks would likely be shot on sight by other survivors.
Also, the remains of the Moon are still in orbit and will provide a constant source of large-scale impact events. Their sheer number means that one of them eventually WILL cause a massive extinction of whatever life still lingers. Consider that the extinction causes by TET already rivals the Permian-Triassic one and not just Humanity, but all remaining multi-cellar organisms are living on borrowed time.
The remains of the moon seem to have settled down in an orbit around each other, and will probably just re-merge into a Moon 2.0.
There may be no real nuclear fall-out or toxic waste. The radiation zones are fake, and Beech makes no mention of humans having used nukes during the war. The craters seen may have been left by pieces of the moon The ecological disaster seems to have been caused by the moon being fractured more than anything else.
There almost has to be some, but it's likely that a significant number of the radiation zones are fakes to keep the techs separated. During the motorcycle Scenery Gorn montage, Jack blows past what appears to be an Ohio-class SSBN with all her missile hatches open, so humanity popped off at least some nukes, even if they didn't launch everything.
The one great horror that remains is genetic diversity, or more precisely, the lack thereof. The Jacks and Vikas can't help that no matter how many they are, and the scavs can provide prime genetic material only if the radiation zones are fake. Even worse, the drones are a Keystone Army, and even if the bubblecraft still work, they will soon run out of fuel. Too bad, they would have come in handy when trying to prevent inbreeding in the long run.