While I don't mind the surfing quarter, I still enjoy the final battle of the TV series much more than the movie version.
In the TV series, it was clear that the "good guy" fleet was the aggressor and the goal was to commit genocide against the Vajra with the intend of occupying their planet as a colony. And the irony continues, in response, Vajra (with the help of Galaxy) used Ai Oboeteimasu Ka to disorient the human assault force. A taste of their own medicine for those pesky human. That was the crowning moment of the TV series for me.
Also lacking in the movie were the nods to other pieces of Macross work. Luca unleashing his ghosts to use the "Sharon Apple" AI for the final battle. And Minmay picture in the pendent.
Battle-action wise, nothing trumps the awesomeness of Macross Battle vs. Macross Battle in assault mode (even a surfing quarter). Then there was Konig monster blasting Galaxy bridge (point blank range face blast). Alto x Brera aerobatic ballet finished with a 360 area sweep, then followed up with the coup de "grace"
Frontier/Vajra queen hybrid just doesn't do it for me. =(