That's a legitimate critique. I myself enjoyed the Cognate arc, I felt it really brought a fuller understanding of the time between "our" present and his dystopian future.
I'll admit I was highly skeptical of "Vampires" being brought into Alita's universe, but they were handled extremely well. Vilma/Caerula is a great addiction to the cast, IMO. It did leave me aching for more story with the main cast, but when it ended I was quite satisfied.
The quarter and semi-finals of the Z.O.T.T. have been awesome, I can't wait for Toji and Zekka to face the Venus team....