My biggest criticism of Frontier would be that it spends a little too much time playing with and subverting tropes, time which could've been used to help explain the story more and not make the ending feel a bit rushed.
Also, as much as I like her, I wonder if the way Sheryl just about became the Macross version of the Fonz (creators and fans liked her so much they expanded her role) hurt a few others in the character development department?