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?