Personally, I think m11 are ending up together, but I can’t get Millie clearly not being very satisfied with her ending out of my mind and what that means because I always thought her perfect ending would be them being endgame. And I know maybe we can take that as proof that they most likely aren’t but I genuinely think they will be at the very end. Maybe she just knows that their relationship is written terribly so it’s half assed or maybe like - someone else joked - her frontal lobe developed, and she doesn’t ship them like that anymore and realized what that type of ending for El really means. 
I do think it’s kinda hilarious how unserious her and Noah are being in their interviews, especially regarding Mike and both El and Will being in love with him. Like this interview genuinely gave me a full body laugh when I watched it https://x.com/bylerity/status/2005557248375021882?s=61&t=f3gxMlccjR3oQ5hW3qKitQ
No, they're doomed. Their "romance" is founded on the shared trauma which brought them together. This is the underlying reason for Jonathan and Nancy's break-up. Mike and El won't be an exception. That's blatantly inconsistent writing, especially with how their relationship is rife with issues and hastily patched together with Will's love confession for Mike as El.
El was in a relationship before she knew her real name (Jane). Before she knew her favorite colors and her style and what she liked and could fully articulate herself. Mike liked that a girl was interested in him, especially a girl who walked out of the fantasies he escaped reality in. Due to his sense of responsibility and guilt, he committed to be being El's guide and protector outside the lab. A role that he's increasingly not needed to fulfill, as El grows more independent and different from that little girl from years back. Because he built his identity around his role in respect to El, Mike was stuck in a rut, until Will reminded him of what he's capable of as an individual. How much Mike means to those around him.
These two fall back on each other during times of instability, because they find comfort and security in each other. However, during times of stability, they fall apart. That's because their one commonality isn't shared interests or deep friendship. It's trauma.
El and Mike need to break-up. If not by a formal conversation, then someone having the courage to leave before falling back on each other during the next dangerous situation, i.e. running from the military. It seems like El's going to be the one to initiate that, given the timing. This sacrifice would become meaningless if they reunited during the epilogue.
MBB's reaction to El's ending is likely due to the fact that El is separated from her friends and family. She has to start all over again who-knows-where. Maybe she becomes an explorer just like Henry? While El likely isn't alone, probably with Kali, I understand why MBB would find it a jarring ending. All that--and she can't even celebrate with her friends. However, El is a character not meant for a conventional life. It's fitting.
