I have a personal attachment to meowrails as they were one of my first Homestuck OTPs and a huge comfort at one point in time. But despite my biases, I am fully aware their relationship is unhealthy and not an ideal moiraillegiance. Like every relationship, there were a lot of flaws that came from both sides of the party, but that doesn't mean it was all bad. They clearly did their best to understand one another and protect each other the best they could.
Equius' controlling nature absolutely comes from the fact he is constantly riding the caste system rules but also comes from a place of trying to genuinely protect Nepeta. It's nuanced, he saw what was going on in the Flarp sessions and it's understandable he didn't want her to join in on those, but then he would also turn around and tell her not to curse like she was a wiggler or something. I'm not really sure what Nepeta saw in him, but one of the purposes of a moirail is to help a troll be the best version of themself, so perhaps she wanted to help him loosen up and be someone that wasn't so tied to the caste system.
Both characters stay in this relationship as they feel it's some sort of necessity, most likely an idea pushed onto them by Alternian society. They played along with what the other wanted to do even if they didn't want to do it themself, that was more like setting a boundary rather than taking complete control in my opinion, but even with the rules set in stone in this relationship they were still able to be apart from each other and do their own things. I think to say their relationship is all bad and no good because of Equius' toxic traits isn't fair, Equius does a lot of things wrong in the comic but he also grew up in a society where he was taught these behaviors were ok. Does that justify him? Not at all, but he is only a kid during all of this and so is Nepeta.
It's easy to forget the trolls are children for most of the comic, they aren't exactly built like children nor do their behaviors really 100% match up with that of a 13 year old (in my opinion). But this was a relationship between 2 13 year olds who were trying to navigate a world that wasn't built for something they were trying to be, especially when one of them is a stickler for rules and the other is more rebellious. However despite the "it's how they grew up" argument, I do understand that multiple characters in the comic deconstruct this concept even in front of Equius' face (including Nepeta herself), but he is too stubborn and stuck in his ways to listen.
I think the biggest problem of their relationship is probably the fact Nepeta was staying in a relationship that clearly didn't meet her standards or make her happy. While a good portion of Equius commands come from trying to keep her safe and she is aware of it, she is consistently seen being annoyed with him as a result. She is isolated from her other friends and even crush because of Equius' deep desire to keep her safe, he never took any time to really listen to her. Nepeta was the better half of this relationship as she was able to pacify him as a moirail should, but she wasn't good in a sense that she was hurting herself by staying with this troll who frustrated her more than not. A moiraillegiance should benefit both parties, not just one, but this moiraillegiance was more in Equius favor rather than Nepeta's.
Yes, Nepeta was benefitted by the fact she was kept safe but even this shoots the relationship in the head when Equius still failed to keep her safe. I also think it's interesting that, in a way, their classpects could even play a part into the detriment of their relationship.
I think what they needed in order to become the ideal moiraillegiance was more time, but both of their lives were cut short. They didn't have enough time to become better for each other or even see their faults in how they behaved. To say they were completely bad for each other is wrong, but to say they were perfect isn't correct either. But I see most people only blaming Equius for the failure of their relationship when it is both of their faults. For Equius, he ruined it by being selfish, overbearing, and controlling, but for Nepeta, she ruined it by not allowing herself to turn away from the relationship and find something better for herself. One was an act of selfishness and the other was an act of selflessness, too much of both will destroy any relationship.
But this is just my personal interpretation, I haven't reread the comic in awhile. Thanks for reading if you've made it this far. :)
Even if the world chooses to become my enemy, I will fight like I always have.