Eleven and Will certainly have not had as much time together to build a relationship as many of the other characters on the show but, with their shared traumatic backgrounds and experience with the Upside Down, you would think they'd get along better.
But Will and Eleven don't take the time to get to know one another even when they are finally given the opportunity (mostly in season three of Stranger Things). Their relationship is solely based on the fact that they are friends with the same people, rather than the fact that they are actually friends with one another.
Leaving Will At The Radio
When Dustin finally returns from science camp in season three the whole gang goes out on a very long hike so that Dustin can construct his radio tower so he can speak with his camp girlfriend Susie.
It takes a bit longer than the others were expecting it to and, in the end, everyone leaves Dustin alone with his project, and with Will. Eleven is much too interested in being with her boyfriend Mike to start attempting to build a meaningful relationship with the newly returned and newly "normal" Will Byers.
Eleven Spying On Will
Max and Eleven decide it might be a good idea to use Eleven's powers to spy on the boys they are dating. When they take on this newest endeavor Will is also at Mike's house, in Mike's basement, while Lucas and Mike try and decide how best to understand the girls around them. Will has no interest in their complaining, but he's still present and is spied upon none-the-less. If you were really friends with someone, if you really trusted them, you wouldn't spy on them.
If Eleven was really friends with Will she would stop spying as soon as she realized he was also present in the basement and had nothing to do with either of the breakups.
Didn't Meet Until End of Season Two
It can be hard to build a lasting relationship in such a short amount of time, and that seems to certainly be the case for Will and Eleven. While Will is only missing for season one, Eleven is hiding at Hopper's for most of season two.
This means that Will and Eleven have only had season three to build their friendship and, unfortunately for Will, Eleven was a bit distracted by Mike in season three. They can't be real friends yet because they haven't had the time to get to know one another.
Don't Spend Time Together
Even after Eleven and Will meet (Eleven having saved Will's life) the pair don't spend time together. Will is busy playing Dungeons and Dragons and Eleven is busy saving the world and spending time with Mike.
It's hard to build a relationship, even after you meet one another if you don't spend any meaningful time together, whether as a pair or as part of the larger group.
Will Overshadowed Eleven
In much of season one Will's disappearance overshadows Eleven's presence as well as her needs. It's hard to want to be friends with someone who complicated an important turning point in your life.
It's clear in season one that Lucas and Dustin care more about Will than El and that certainly could not have conjured friendly feelings between El and the missing "party" member. Eleven is building her own friendships with the boys around her and doesn't have time to put effort into a relationship with Will.
Different Interests
There is very little for Will and Eleven to connect on (other than the Upside Down) when they do spend time together. Will is still obsessed with Dungeons and Dragons, a game Eleven has never played.
Will missed the bonding in season one between Eleven and the rest of the "party" and he's obviously not yet interested in romantic relationships or the mall. Despite the friendship that could develop between El and Will there's very little for the pair to use as a jumping-off point.
Emotionally Stunted
It was hard enough in season one for Eleven to build a relationship with Mike, Lucas, and Dustin, and those boys have not been tormented and kidnapped. Eleven's past was complicated, she was both tortured and kidnapped. Her emotional growth was stunted, just as Will's is when he returns from the Upside Down.
He's still much younger than Dustin, Lucas, and Mike seem to be. While they should be able to relate in terms of their struggling emotional growth, it's this stunted emotional element that hinders Eleven and Will's friendship.
They Compete For Mike's Attention
Will, as Mike's best friend and Eleven, as Mike's girlfriend, are competing against one another for Mike's attention. This automatically sets the pair up as competitors rather than friends.
They are both after the same thing, Mike's time which is finite and must be split between them. This competition doesn't exactly lead to friendly feelings or understanding, despite the shared trauma in both El and Will's pasts.
They Remind Each Other of the Upside Down
Will and Eleven are both traumatized children. They both suffered due to the actions of the same lab and scientists. While this could bond them, instead it pushes them apart.
Both want to move on and live relatively normal lives, but each stands as a reminder to the other of the experiences they have suffered through. Rather than being a comfort to one another Will and Eleven act as triggers, complicating terrible experiences and memories every single day of their lives.
They Move Away Together
At the end of Stranger Things season, three fans watch as Joyce Byers drives away from Hawkins with her sons Jonathan and Will, as well as Eleven, in the back of her car.
At the end of season three, Will and Eleven are set up to embrace the relationship of siblings rather than that of friends. While you can get along with your siblings, enjoy them, spend time together, the fact that you are siblings will always take top billing when it comes to defining the relationship. Will and Eleven are far more like brother and sister than they are like friends.