Season 2's seventh episode hints at an X-Men-like Season 3
There are a few dangling threads left hanging out there in the episode "Chapter 7: The Lost Sister," but most people who binged watched Season 2 can tell you that the it felt like an episode from a completely different series. Taking the action out of Hawkins, Eleven meets Eight (Kali) and her band of misfits that have been travelling around killing people involved in the MK Ultra experiments. Not only that, but the person they happen to attack thanks to Eleven’s tracking abilities suggests that Doctor Brenner (“Papa”) is still alive and survived the Demogorgon jumping on him in Season 1.
Eleven decides she needs to help her friends and ditches Kali, but the seeds for the third season are planted: there are more psychic kids out there and the person responsible for making them is still at large, motivations unknown. Let’s make the assumption that the children were numbered by age at Hawkins Lab, which means One -- whomever it is -- could end up being Terry Ives, Eleven's biological mother, or it could be a child that has since grown into adulthood. Maybe One died. Somehow, by experimenting with pregnant women and children, Brenner unlocked several psychic powers that he intended to use. Now, those children are all rebelling, at least whichever other kids are alive.
The only bad part about there being multiple MK Ultra kids running around the world is that Stranger Things thrives in Hawkins with the main kids. Shifting Eleven to Chicago, or if they send her elsewhere in the 1980s world to find other sisters and brothers, is going to feel just as weird as "The Lost Sister" did. However, that doesn’t mean the show isn't setting up for a battle between psychic kids and Brenner. If the government scientist lived, and he continues his work, we could end up with a Kali/Eleven against other sisters showdown, who knows?
Well, Murray, the investigator hired by Barb’s parents (and who closes down Hawkins Labs) would. Netflix's official Stranger Things aftershow suggested that Murray has a backstory that we don’t get to in Season 2, and maybe Season 3 is his time to take what he knows about Hawkins experiments and find the other psy-ops kids.