Jesse and Petra may SEEM like they're meant to be--and they are. The only problem is that there are other people who qualify as a match for either of them. I hope I cause no offense to those who ship the ones I am about to list; this is only for the good of Jetra. So if that's all, let's start.
Lukas may be a good guy in the actual plot, but in terms of Jetra, he might not be so good after all. He seems to have feelings for Petra, and she accepts it back. Petra even mentions to Jesse that Lukas has come through for her in certain situations, so it basically confirms any sort of relationship between them.
This ship is actually SUPER popular. Come to think of it, it might even exceed Jetra's popularity. (HOPEFULLY NOT!) Why this is a necessary danger to mention is because at first, Lukas is an enemy to Jesse. But later on, he becomes more of a friend. From what I've learned, when an enemy becomes a friend, they can become "more of a friend" real soon. So yeah, Lukas is a huge threat to Jetra.
The big, LOVABLE, guy of the group, Axel has shown his concern for Petra more than once. But, unlike she does with Lukas, Petra doesn't seem to pay much attention to it. She still likes him as a friend though, so not a complete loss for the Axtra shippers.
She cares for Jesse a lot, almost to a fault. The worst part is, it seems to be canon in the game, according to Episode 4, when Olivia's trying to get the barge to work. Thankfully, it's not too popular with the fandom. So, for now, Jesse identifies her as a friend, like Petra does with Axel.
Let's face it: sometimes, X-over characters can be lethal to a ship if it's popular enough. Be they from a different game, T.V. show, movie, anything could happen. By sheer luck, no x-over ships have busted into Jetra, so I'd say they only have the characters inside Minecraft Story Mode to worry about.
The Anti-Jetra Creeper Spy
Make no mistake: everyone HATES creepers. So why is he here then? Well, I have a theory that there's a certain creeper who is able to respawn just to ruin a moment between Jesse and Petra. He is seen leading some of his nasty friends to the bridge, falling behind Jesse when he was (MAYBE!) about to go for a mid-air kiss, and when Petra shows Jesse her wither sickness, the same creeper pops in to trap Jesse in that hole. So yeah, he's pretty much evil.
Isa the Founder
Weird but true: people ship Jesse with the Founder of Sky City. No one looks to deeply into it though, because she has Milo to keep her occupied. Even so, like Olivia, it might be canon in the game. Jesse has an emotional talk with her if he chooses to help Ivor, and he also has the choice to save her. Now that I'm looking at it more clearly, it's really up to the player to decide if these two are a thing or not.
Similar to the Isa-Jesse effect, Milo and Petra are shipped. However, this ship is not popular. The possibility is there, but it's not popular, so not too big of a deal when it should be.
Due to the last episode of Season 1, Nell has REALLY put up a fight to be Jesse's significant other. She helps Jesse get the wheat he needs for bread to feed Facemeat, he has the option to save her, and she even moves into his town and helps on certain occasions. Luckily, Jesse doesn't pay much attention to these actions, so this is a bit one-sided.
This one is a bit of a bigger problem, because Jack is, as said, Petra's hero. What's more, he may be making a few moves on her, ones that are SURE to lead her away from Jesse. The only protection Jetra has against this ship, is on how Jesse thinks of Jack himself. Only if Jesse dislikes Jack in the slightest, can the ship be saved.
One that wasn't expected, but it came up anyway: the old "intern/boss" relationship. Obviously, RADAR likes Jesse enough. What happens if Jesse notices these feelings? (Then again, there's always the fanon ship, Radki)
And that's all the competiton this match made in Mojang has to face! Notch forbid that I'll have to add to this list. Bye for now!