To be honest, I kind of like the ending leaving the matter of Gauna origins unanswered. The mystery is kind of part of what makes the Gauna interesting, I feel like.
That said, I think it would've indeed been interesting to see the matter of Gauna communication explored a little further.
Though I kind of doubt the Gauna have been completely exterminated from the universe. So that might not be completely off the table yet.
Also, Tsugumi's revival actually made sense to me. Or more like, I sorta predicted it. All the necessary pieces were already introduced to the story.
I rather would've been pissed had Shizuka's pseudo-clone been forgotten about.
No, the real asspull was the accidental terraforming of Lem-VII. Though it's not really a biggie in my book.
The only thing for me is that I think it would've been really interesting to see their life together unfold with her retaining her chimera form.
And the one changing(?) genders was Yuhata, wasn't it?
Lastly, the line about the Nodoka/Izana promise kind of smells of sequel baiting.