Once the player sees that Mystina can't be sent up to Valhalla, it would be a good guess to assume she'll be important to the plot. In fact, it's safe to say that without Mystina, the A ending would fall apart completely. Her story explains everything about half-elves and Odin, which is vital for the ending. Certainly, in a game full of sorceresses, any one of them could have served the same purpose, but in my opinion Mystina's the best one for it. Her being a graduate of the Flenceburg Academy establishes her relationship with Lezard, and her thirst for knowledge allows her story to turn into exposition rather than purely about her, as most of the other einherjar's stories are.
As I said above, this sets up the A ending perfectly. Lezard and Mystina work together to save Lenneth, and thanks to their conversation in Chapter 5 the player understands what it means when Lenneth's newfound ability to grow is revealed. Furthermore, with the relationship between Lezard and Mystina established, it's clear she acts as a foil to him in restoring Lenneth. While his motivations are selfish, as he explains in his scene with her, she wants to save Lenneth for Lenneth's sake.
As well as Mystina works for the ending, there is one rather large plot hole, and that is the Lost City of Dipan. When Lenneth is sent back in time, she sees Hrist, along with an earlier incarnation of Arngrim and a mage that looks suspiciously like Mystina. While Arngrim's appearance there establishes his relationship with Hrist, there's no reason Mystina should be there. In fact, no mention of her presence is made at all, in Valkyrie Profile: Lenneth or the sequel, Valkyrie Profile 2: Silmeria (which considerably expands Arngrim's role). In Dipan, any sorceress would have done the job, so why Mystina? Why use one of the story-important, required characters rather than some random NPC or another of Lenneth's einherjar?
This is a mystery of the game I've never been able to solve. It seems very strange to me that they would use Mystina alongside Arngrim there when they're both very important in the ending, as well as Arngrim's continued role in the sequel. My best guess is that they needed someone to serve as Hrist's einherjar and went with previous incarnations of Lenneth's so they wouldn't have to design new ones or use NPCs, but it makes it very confusing for the player.