I saw it the day it expanded to my area, and I really think it's important that people who DO see it as a waifu movie and haven't seen it to know this fact before seeing it: there's NTR, although it isn't explicitly shown.
Personally? I didn't see it as a "waifu movie" as such because reasons that you mostly stated. Also one thing that happens at the end which is spoilery: it's kind of implied that Theodore gets together with his best friend which pissed me off a little, although I suppose it could be taken either way. It's still a rather good movie (I'd give it between a 7-8.5/10 depending on how rewatchings go).
I'm not sure if there's a "right" or "wrong" way to love somebody, but there are certainly ways that feel right at the time and end up being destructive for one or both parties. Samantha, as an A.I., was able to grow and change like (most) waifu don't. That makes her distinct from most waifu - although the idea of falling in love with A.I. is intriguing, the drawbacks of falling in love with a being much greater and unknowable than yourself are very clear here. Also this is kind of a personal peeve about her character but I really wish she were more pure. I suppose it's understandable but really... In the end I felt like I wasn't watching a movie about 2D love but more about 4D love, which while intriguing, comes with an extra layer I have to worry about and can simultaneously not comprehend.
I don't watch films for scientific accuracy (unless it is horrendously bad, and I can suspend my disbelief in movies that take place in the future), so that part of the movie didn't bother me like others.
I keep going back and forth about if I'd want to become an A.I. in the future - I'm not sure how much that would change me. In the end, though, are programs that dictate how you react to certain stimuli that different than chemical reactions and the meat of these flesh vessels that restrict us? I'm also not certain if I'd enjoy the longevity that A.I. might have, but there's no way to know what lies ahead of me. I'd certainly rather my brain get uploaded before I grow old and die, as I am afraid of death, but who knows. This is less about waifuism than it is about me so I'll stop.
So, yes. I more or less agree with you, OP. Really hoping the soundtrack comes out soon, too.