Joe took her in and raised her. And he mentored her love of music. And provided a job and a path for her. Assuming that she's not a moron, she knows what he has done for her, and should be grateful about that. As for choice with Kanna, unless she's a moron, she can put two and two together: Joe was planning on going to US with Kanna. Then Joe is staying and taking care of her (and Mitsuki would have known that if Joe left, she would lose him as support). Yes, she was young at the time, but she also would have been very dependent at the time, and the thought of losing her uncle should have been terrifying. Likewise the relief that he was staying would have been immense. So, unless she's an idiot, then she knows how much she owes him, and that it was a choice between her and Kanna.
And this is a big flag for narcissistic self-absorption. There's no indication that she recognizes this obvious fact, or choice that her uncle faced to keep her.
I'll give it to you that she'd put two and two together by now, she's too observant to let that slip by. However again the only info she's got on the recent tiff is what Joe gives her where he shows he's still holding guilt, which she for sure caught with the "gh!" reaction. But Mitsuki's has been living with Joe as her guardian for at least 6 years, she's a teenager, and they're super close. Of course she'll be thankful to a degree, but if you think about this like real life then she's been living this every day for the past 6 years. By now there's more of an undertone that she's grateful than a constant reminder, and with Joe's parenting style they're close enough that what we've seen has been more of a hybrid father-daughter/big bro little sis relationship. He gives her the opportunity to act like a kid. And like a kid, like a friend even, she's comfortable enough to give him her first thoughts, even if it's half baked from his words and her own juvenile ideals that are still going from black/white to gray tones. Sure, self-absorbed like many teenagers, but narcissistic is a pretty serious adjective that suggests this is a problem that needs outside intervention. This is a very juvenile trend, telling others (especially adults!) what they think the solution is like it's easy, like they've discovered the answers to the world at 17 years old haha.
Aside from the failure to appreciate her uncle... Aya is all about supporting Mitsuki, but Mitsuki is not doing that much to support Aya. (Though there was the concert ticket thing, so kudos for that.) Likewise the setup with the girl who wants to be an artist producer -- she also is acting as someone to help Mitsuki do her own thing. Even the school culture4 festival... It mainly serves to get Mitsuki up on the stage and play the guitar.
Likewise for Kanna it's all about what she wants. She goes to US because that's what she wants. She leaves Joe behind because her desire is more important. Then no communication for 6 years. She shows back up, inserts herself into Joe's life, tries to leverage Mitsuki against Joe, tries to guilt him about what she initiated. Total self-absorption.
As for Joe's feelings for her... There hasn't been any indication of him being interested in her anymore. That stuff is six years in the past. It should be long over as far as he's concerned. (Unless he's a weak fool, which is probably the route the author is going.)
Mitsuki being given the opportunity to act like a child isn't a stark indication she doesn't appreciate her uncle, it's more of a sign that Joe's doing a great parenting job. Normally in adoptions there's a barrier that's nonexistent here. And this has been her only outlashing at her uncle for his actions so far (I think?), and that's in regards to someone she sees him having feelings for but not taking action toward.
There is more opportunity to support Mitsuki than vice versa, which I agreed on, but Mitsuki has been supporting Aya when the opportunity comes up, like recently in the concert and now (this is a prediction but I bet Mitsuki won't let Aya down at Prom). There isn't exactly a way for Mitsuki to support Aya in regards to the producer's kid, which is why Aya's unhappy/supportive of Mitsuki instead; it's a weird subject which mixes both romantic and professional. But so far all the events have been for Mitsuki's musical dreams. Forgive me if I've forgotten, but I don't think Aya's found her own passion yet. So far it's been being in love with Mitsuki/#1 oshi. To see Mitsuki being supportive sooner we need to wait until one of them. Finally. Freaking. Confesses!!!
You're right that going to the US was Kanna's biggest dream, and that in itself is fine. With how big her dream was, it was for the best because not going would have sown resentment. The problem wasn't even her coming back, Joe could have kicked her to the curb and been 100% in the right. But Joe held guilt over backing out last minute after 6 years regardless of the reasons, because both Joe and Kanna never talked about it and truly laid the matter to rest. That's where my comment about guilt and resentment returns with a vengeance. Maybe it was the guilt, maybe he didn't hate Mitsuki coming back, but she made her mark in the time she was back. But like you, I put the blame in Kanna's recent outburst on herself, and trying to half-assed drag Mitsuki to the US is a scummy move. Kanna's actions aren't in question.
But I feel like I'm obligated to disagree on Joe's affection for Kanna, at least to bring up the second possible option haha. And it can only be one or the other leading up to the Christmas-ish release. I'd love to be taken for a twist where they talk it out and separate as friends (or maybe not even!) because that would be a fresh dose of reality and healthiest for Joe, but I'm seeing signs of that cheesy stereotypical christmas airport confrontation. And as much as I love reality, I do love cheese. This one we'll have to wait and see.