Yeah, it's certainly got a few issues. As you mentioned in the review, the Daitanix plots did get kind of repetitive. It didn't take away from my enjoyment, but there was a hint of déjà vu after a while.
The only thing that really bugged me though during my re-watch was the half-assed resolution of Hyuuga's story.
((Spoilers for those who haven't seen Ginga))
Suddenly getting his Earth Power back just through... force of will or whatever. I wasn't real into that. To me, defeating Zahab, but giving up his Earth Power and his home in the process would've been a much more impactful ending. War has consequences, there are losses on both sides. It would've been nice to see the show use Hyuuga's situation to reflect that. Have him (and the others who would naturally stand by him) unable to return to Ginga Forest, forced to find a new place in the world.