Ok that ending made no sense

Won't explain it next season I bet. Because it would be some other bullshit.
Probably, Satan finding loopholes to and that end of the world is a prophecy that can't be cancelled, only delayed.
Notice how this time around the Crows and Red skies appear much, much earlier for the new Anti-christ, right about the time when he killed his Baby-sitter and the Satan worshippers immediately showed-up?

There had to be something special about the two young people to get selected in the first place. Because we know now, that the evil Corporation picked them - maybe they were meant to be Plan B all the time if Micheal fails or dies.

At least it gave some closing on the first three episodes. Even though, I liked the randomness of building them up and killing them in episode 3.

I think it was explained in the first episode that Tim was selected because he went onto one of those ancestry DNA sites and the people he sent the DNA info to found that he had the perfect genes. Now, maybe his immediate family wasn't into devil/satan worshiping, but maybe an ancestor or two were. Same thing with Emily. I believe Emily was chosen because she did the same thing with the ancestry sites and they traced her family tree far back enough to find devil/satan worshiping at some point. So maybe Tim and Emily carried the perfect genes from their ancestors, and those perfect genes were obviously to create a new antichrist if Michael failed. But in the timeline we saw, Tim and Emily were killed off before they could create the new antichrist. When Mallory went back in time though, she only prevented Michael becoming the antichrist and stopping his apocalypse. Mallory didn't prevent Tim and Emily creating another one. So the two ended up crossing paths a different way and then they created a new antichrist. So all that really happened was that the apocalypse got delayed, but is eventually still going to happen. And the whole antichrist thing is on an endless loop. When one dies and the timeline is reset, the antichrist is reborn or something through another child/person.

Another thing I'm thinking of, is maybe there was no motive or reason for why Tim and Emily were chosen to create the new antichrist. Maybe they were chosen just because. Maybe evil doesn't really need a motive/reason for who would be the ones to bring the new antichrist into the world. It just does stuff just because and evil decided to randomly choose Tim and Emily's child in this new timeline.

I just knew something was up with Tim and Emily though when they decided to show them cross paths in the new timeline and then show them having a kid. I figured that once we seen the two in the hospital and their baby was born in the "one year later" scene, there would be something off with the kid.

I think it's mostly like another person said, the apocalypse can pushed at bay, but that's all. Only delayed, never eradicated.

I'd say Timothy and Emily's genes played a huge part. But I don't think they were necessarily special. Because when they arrived, we saw other young attractives being killed for coitus. They were easily another back-up pair. And maybe not wanting these people to reproduce another "average" mouth to feed when they might be needed to replace the Antichrist, that could be a big reason for the no sex rule.

And while the Antichrist probably, in this TV universe, needs some sort of special way of coming into existence, it's probably not so specific as how Michael came to be, ie it didn't have to be that particular house and those particular parents. Just something dark, twisted, and evil. And who knows what darkness Timothy and Emily have seen in this alternate world where they've had a kid.

Maybe Emily was raped by some other malevolent ghost at some point during her marriage. Tim may not be the father.

There's a theory out there (that popped up during the season actually) that those two (Emily and Timothy I think their names were) are or are somehow related to Kit's two children from Asylum (their genders and races fit). Maybe they'll revisit that in the future if they have an Asylum crossover.