This is certainly how it came across to me.
I realize that the intent, poorly written and directed as it was, has them as truly being in love, but it never seemed that way.
They knew each other for a week, at a time they were both going through severely traumatic events. Mike was desperately searching for his missing best friend, and El was trying to escape her abusers who she already saw execute someone who dared to help her. Mike took care of and sheltered El while she helped find Will. This resulted in them bonding over their trauma, seeking comfort in each other.
Then they're separated for a year after El sacrificed herself to save Mike and the others from the demogorgon. Mike thinks she's dead and feels guilty. He copes by reaching out to her in the hopes that he finds a sign of her like he did with Will. El spends her year watching soap operas, learning an inaccurate idea of what love looks like from TV while sneaking glimpses of Mike through the void.
They build up ideal versions of each other in their minds. Having never known each other outside of that week of trauma, neither one knew how the other's true self. Hell, El didn't know her own true self. But it ends up with them ending up in a train wreck of a relationship after the emotional reunion settles into normalcy. Their true selves don't match up with how they envisioned each other.
This is why their relationship failed. This is why it never looks like they made any genuine progress towards fixing their problems. The Duffers can gloss over it all they want and handwave their problems into them being magically ok, but a discerning viewer sees through that claim. El only ever wanted a normal life, but Mike always saw her as a superhero. In her desperation to fix things with him and trauma from the bullying she experienced, she willingly goes to "be a superhero again." On the surface, it's so she can save her friends in Hawkins, but, with how she worded the note to Mike, it's clear that she considers this the only way to make Mike love her. Mike gives her value, but she's afraid she has to be the superhero he sees her as to keep it (or get it back in this case).
For his part, Mike feels like a worthless nobody next to El, unworthy of her affections. He's convinced she will eventually grow tired of him and leave him or resent him, mirroring what Jonathan was going through with Nancy. So, he avoids being too committal, never saying he loves her, despite El explicitly telling him that she wants him to. El gives him value, but he's convinced it'll eventually be stripped away.
It's a bit confusing, in retrospect, as it is exactly the same sort of situation that we're later told Will is in with Mike. Will's "crush" on Mike is harmful to him because he's convinced himself that he only has worth if Mike loves him. That's considered problematic to the point that he has to cast off those feeling before he can love himself. However, with Mike and El, it's ok. Nevermind that Mike needs Will to lie to him, giving El credit for his own feelings, to remind him that he does have value. Nevermind that El learns that seeing herself as a superhero or monster is unrealistic, and that real people have both good and bad in them. Nevermind that Mike "saves" El by reminding her that she's his superhero, but only after strong urging by Will. Nevermind that it was Will's feelings for Mike that saved the day and Mike and El's relationship.
But, whatever, with our star-crossed lovers, it's different because they do love each other, right? (It has nothing at all to do with Will being gay, right? No, of course not...). Mike and El are in love, but the world is out to get them.
So why don't they act like it? Why do they constantly lie to each other? Why do they go from acting like incompatible relationships, like Karen and Ted or Steve and Nancy, towards acting like a couple that got together based on trauma but whose relationship crumbled, like Jonathan and Nancy? Why did it make sense for Nancy and Jonathan to realize they were better off breaking up, but not Mike and El?
We had two scenes where a couple was facing impending tragedy. Nancy and Jonathan had a genuinely heartfelt scene when they thought they were about to die. They opened up to each other and were emotionally honest for what seems to be the first time since season 2. In one of the few successes of season 5, the symbolism of their relationship suffocating them as the goop built up in the room worked brilliantly, as did the danger ceasing the moment they cleared the air and had arguably the sweetest breakup I've ever seen on screen.
But compare that to Mike and El's void scene. It's melodramatic, with stiff acting and highly dubious dialogue. The Duffers will never convince me that Mike, of all people, understood El the most. Not Hopper? Not Kali? Not Will? Not Max? The girl who told Hopper, the man who adopted her, that she's not his daughter, returning the hair tie to him, somehow sees her relationship with Mike as real. The suggestion that Hopper didn't see her as his daughter, only using her as a replacement, is insulting when she still clings to Mike in her darkest moment, as if that relationship was more genuine.
It's insulting, not only to the snubbed characters, but to the audience, as well. It depends on taking in this highly skewed take on their relationship without question. Anyone who watched their relationship with a critical eye would know it's bull.
I suppose that, in the end, it was made clear that this show wasn't really made for viewers with a critical eye.