When I finished watching the Macross Frontier TV series, I felt it succeeded at most of the things it tried to achieve, but could have benefited from giving a couple of them more attention during the climax. I came to this movie expecting it to be mostly reused animation from the last several TV episodes with some new scenes that would enhance certain parts of the story. That's not what this is. Wings of Farewell not only has all-new animation, it's a significant reworking of the events of the series. I don't think it's even a case where you could watch the series up to acertain point and then decide to cap things off with either the TV or movie ending, since some earlier events from the TV series have already been retconned by the time this second movie starts.
The good news is that it improves the weak areas of the TV series, making Alto a more proactive and capable protagonist and giving a more satisfying arc to his story. It pays off the romance arc in a more definitive way. It also adds some memorable new action and performance scenes that all have excellent animation.
The bad news is that this comes at the expense of the things the TV series did well. The war and conspiracy story arcs aren't handled nearly as well in this movie. Upcoming developments are telegraphed and too much is bluntly stated in expository dialogue, robbing it of the tension and build-up that were strengths of the TV version. Also the most memorable scenes from the TV climax are missing entirely, since events are playing out differently by that point.
Wings of Farewell is another great ending to Frontier, but just like the TV version it feels like neither is the definitive ending. So much is changed that I doubt it would be possible to splice together a fan edit of all the best parts from the TV and movies versions to reach something that pays off every story arc in the way it deserves. So I'm left feeling that the only way to have the ultimate Macross Frontier experience is to watch both versions and then blend them together inside you head.