The movies have the same relationship to Macross Frontier that 'Do You Remember Love' has to the original MacrossSpecifically not only is it an alternate continuity its a pair of movies that were made in the TV series timeline at some point after the series ended. The painting of the Galaxy fleet as more ambiguous in their motives (it comes across more that Frontier and Galaxy fleets are rivals vying to be the first to gain control of the Vajra as a source of fold quartz) is due to shifting political climate.
The events in The Wings Of Goodbye parallel the events of the iCarly episode iOMG onward.Alto chose Sheryl on the movie. Freddie got kissed by Sam. Both Ranka and Carly ended up losing their respective male leads. Both Ranka and Carly stayed strong (the latter ends up having her best friends being shipped by her).
After The Wings Of Goodbye ended, Alto ends up in the Megaroad-01.In the movie, Alto folded with the "Vajra Frontier" and gets lost in space too forever. as he was drifting in space unconscious, Hikaru Ichijo found him and treated him back to life. There, he meets Lynn Minmay and became friends. (The reason why they still look the same is because they aged slowly due to being lost in space.) How Alto got back to the Vajra planet though is when Alto helped the Ichijo's get them back on track going there, although the people on Earth still didn't receive the message that they were ok after that.
The Omniscient Council of Vagueness that tried to take over in Vajra in The Wings of Goodbye are Zentradi who were subjected to endless implant experiments in Galaxy and wishes to revenge to both humans and Vajra.At one point of the movie, there was a close up of the who was in the big pod. This picture wasn't lying after all...◊