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I guess that depends. It was certainly *heartbreaking* if you were invested in that subplot (or heck, many others) no further progression, nu cuteness, but tragic ending =/= never happened. Many so called "famous love stories" have tragic endings... tragedy was part of the whole Rs deal since NGE proper.
Rei's presence was still felt through mentions (much to poor ReiQ's extreme confusion), and we pretty much gort the ultimate proof that Shinji actually did pay attention to her as a person (books! Who become a symbol of her individuality like Original!Shinji's cello. Note that books aren't something Shinji brought her, she had them to begin with. It's also a solo activity, not something he also profits/takes part in. And, there's that detail that Anno used to read novels that were popular with women to better understand them which may or may not be related.) and wasn't in it because she looks like Yui or because of "submissive bottom he can order and shape like he wants", because ReiQ would still have been those things. He could just have ordered her to read the books and go full vertigo on her.
When I first saw this movie, it threw me into some ludicrous dispair for days, but the way I was able to... go on and find beauty in that bleakness is that life has good things and bad things, and while the good don't soften out the bad, while you can try your hardest within your limitations and still fail (and I firmly believe this is what Shinji has been doing here) the bad things don't make the good things unimportant. all stoties end with "...and everyone involved died of old age or got blasted when the sun exploded", regardless of some people stopping telling them earlier so... Shinji's struggle and Rei II's progress (of which their relationship was one facet, not more, not less) wasn't meaningless.
As much as I would have liked... actual Rei screen time, the wave of baddass!Rei and Philosophic!Rei we've been having can't be a bad thing.
