Maia is perfect
You all should know it by now
Difficult to point out flaws in people that have almost no character development. One could argue that Anna, for example, had a hideous past, but we only know that she has a past she would like to forget.
Obviously, Shir is a thief, so she has a serious character flaw.
Rhys, arguably, is somewhat selfish and reckless, as he wants to bring all the soldiers with him to rescue Maia and his quest is apparently only for his own interest. Although their intention probably was to make him start fighting for what is right as he learns about the world, it is never made clear. However, he can't be blamed for dumping Lena, as he didn't know he had been promised to her.
As for Phantasy Star IV, all the characters have flaws, because they are j-pop anime/manga stock characters. They have many flaws, but the script takes care to make them become the "bestest characterest everest" in a way to make the readers/watchers/players forget about their arrogance, selfishness, stubborness, silliness, always used as the same cliché comic relief (Alys seems to be abusive, but is kind, just and acts like a mom, sacrificing herself for her "son"; Rune is bully and arrogant, but always trusted and believed the guy he bullied). Most remarkably, criminal past makes the person perfect. Past thieves are always the main heroes and get the princess or magical/unique girl in the end.