There's a moment when Mikhail goes for the head of Brera's VariableFighter in Episode 9. At first, this made no sense, because the head unit of a Variable Fighter only contains sensors and a near useless laser, and the former is only really used in Battroid mode when the cockpit is retracted and covered in armor when transforming into Battroid mode. The trick is, the pilot need only transform into Fighter or GERWALK mode to enable the pilot to use his own vision, as The Hero does in Macross Zero to great effect after he loses his own fighter's head. Meanwhile, the cockpit is actually contained inside the center of mass, which is actually the easier target anyway, so it didn't make sense for him to aim for the head. They weren't trying to kill Brera, they were trying to capture him. When Mikhail goes for the shot, Alto has Brera tied up in hand-to-hand sumo mecha style, with so many intermingled moving parts that part of the reason for the sumo wrestling was to prevent the other from transforming out of Battroid mode, as well as keep them stationary. Thus, if Brera's head got shot off, he'd be completely blind in his current transformation mode, and unable to transform into a different one because Alto was all over him. With a connected shot, Alto would have easily had the upper hand and could have disabled Brera's fighter with a few well-placed point barrier punches.
Ranka Lee is hailed as the Super Dimension Cinderella, but there are even more Princess parallels throughout.
One can easily guess that Nanase might be Sleeping Beauty based on the coma she had in the latter quarter of the series.
Sheryl Nome draws the less obviously from "Rapunzel" she was taken in by a by an Enchantress re: Cyborg partially to spite her ancestors and was trapped in the prison of her own dying body, also it wasn't her hair, which in its own right is very unique, but her Singing Voice that drew her the attention of her prince.
The prince heard Rapunzel before he saw her and that's why he stumbled across her tower.
The ending for the Movies also adds in a parallel to Snow White for Sheryl: an Only Mostly Dead maiden sleeping in a glass "casket," awaiting her true love to come awaken her. One of the cards in the Macross Card Fighter Mobile Phone Game even had Sheryl dressed as her!
Even Alto has something in common with a princess, Kaguya-Hime, both wanted nothing more than to escape that which confined them and return to the Sky.
As of the last movie, Sheryl is the apparent relationship winner, though there were subtle hints all along there is one that stands out; Triangler Fight On Stage! who is the one who sings the line Like how we are friends but you don't love me? it wasn't Sheryl
Also, Ranka is often compared to Linn Minmay of the first series. Guess who lost the Love Triangle in SDF Macross?
On top of that she played the part of Mao. She didn't win either.
In the second movie, Sheryl has a couple of performances where she crossdresses, and cuts a dashingfigure doing so. This seems to be a hint that she's perfect for Alto, especially since one of her costumes looks quite princely.
In the Grand Finale, Ranka comments that the Vajra speak/think with their stomachs. Anyone who's taken singing lessons knows that to sing "properly" and project your voice, you sing from your diaphragm. Where is it located? In your stomach! Thus the fact the Vajra only really notice when Ranka sings or is very loud makes a lot of sense!
Near the end of Ranka's performance of "Niji Iro Kuma Kuma", the camera closes up to Sheryl in the audience as a holographic Ranks gives her a teddy bear. At that point, Ranka is singing the words "the feeling of a little girl will persevere". While the lyrics seem to be referring to Ranka, the creators are actually subtly hinting at the fact that Sheryl as a child was inspired by a performance by Alto. Driven home during the scene where Alto finally realizes this, and Ranka is singing this exact song.
Why Kawamori thought it was obvious that the movies actually ended happily becomes clear when you pay more attention to the final credits song; Ranka and Sheryl are performing a live show together, something they couldn't do if Sheryl wasn't around and the happy nature of the song and performance hints towards Alto also being back.
Sheryl is not the only girl that Grace has infected with the V-type virus, there were nine other girls before her. If you pay attention to the dialouge between them in the tv series and the movie you find out that Sheryl's nickname given to her by Grace and her collegues is Fairy 9. That means that there were essentially 8 other failed projects before her, and of them Sheryl is the only one who had made it the farthest both in life and in their objectives. In other words there were eight other little girls who Grace and her collegues painfully infected with the V-type virus who died before they ever got a chance to really experience life. Evidence of this comes from the Drama CDs where Grace is regrettfully realizes that Sheryl might never get to fall in love, or find anyone that would be able to understand her. This wouldn't be so bad except Grace sounds certain that Sheryl would never be able to live that long, as though its happened before. Grace had done it before to other girls that's why she was able to erase all of her memories of raising Sheryl so easily.
The second Macross Frontier movie has this. After Sheryl falls into coma after watching Alto disappear, Ranka heals her - just like in the series. It is then stated that "Sheryl will wake up when Alto comes back - just like in the series. But there is one crucial difference Alto won't come back in the movie verse - and thus Sheryl will never wake up. By saving Sheryl, Ranka just condemned her to lifelong coma. How is That? Now there is of course a possibility that Sheryl will just wake up on her own, but the prospect of transforming a death into a Fate Worse than Death is definitely there.
Go back and watch the end-credits sequence again. The supposedly comatose Sheryl is mouthing the words to the song at the end, and her earring is glowing. She's already waking up. It's not like Alto died anyway, the Vajra Queen space-folded away before the attack hit. He just has to find a way back to the planet. Once the Queen gets Battle Frontier out of her gut, he can fly back on that or something.