Macross Zero was a little too quickly gone through and slow, boring for most of it. If I recall correctly, the series was only meant to show a prequel to SDF only. It had no real reason for being there. I was amazed that Wikipedia said this because yes, not a lot of people were interested in it. I, being one of them.
Spoiler for The world of Kawamori is confusing, ne?:
As for Frontier: a LOT of crap went down between Kawamori and his producers/scriptwriters/whatnot over how to end the story/triangle. The ending that was chosen didn't suit his ideas, apparently, so he went back and said "I'll make a movie."
As for DYRL: they said it was a retelling of the story... well, if I hadn't watched the first few episodes of SDF before watching the movie, I would've have known why they were in space or what the heck was a Macross. Plus, both storylines were different. Minmei and Hikaru met before they boarded the Macross, whereas movie!Minmei meets him for the first time 5 months out on the journey. It was a little screwed up.
Kawamori (I cannot keep this to myself) loves to give you things you don't want to see. Honestly, I've seen more bad endings from him than I care to count. For once, I thought I'd see a good ending. However, he didn't do it... at least not well. I wouldn't have killed Alto... after all, he said back in the series that he didn't really want to kill Michael, then he goes and... does this.
As for Minmei vs. Misa: no, Misa was more popular when DYRL was released and when SDF reached it's peak, she was the one they adored more. So when the votes were cast, he turned to Hikaru/Misa ending. Personally, that was his BEST ending, because he verbally asked her to marry him.