Shion was a shitty character, now shut your hole.
Care to explain why?
No, but I guess I have to.
Incongruent and disparate portrayal between her personality and profession. One can't be that much of an airhead and be a "top scientist" of any order. She demonstrates none of the mental efficiency that a scientist of her calibre would require to accomplish any task. Further, she has none of the professional drive that would be typical of most in her position. In short, she'd be a really lousy scientist by any realistic measure.
But let's say we suspend disbelief for a moment. Even then, her narrative is surrounded with incompetent people. Look at all the people who work on the project with her. Save for Kevin himself, the entire team responsible for KOS-MOS seems like it couldn't figure out basic arithmetic if it needed to. It's one thing to have a casual and friendly group of scientists working together, but they portray no credibility.
Shion herself is a shining example of this. She has no professional credibility in her character, and she's ill-suited to be a main character to begin with. She's written from the perspective of a dating sim character (as Neal inferred), using the archetype of the dreamy ditz. If we consider all the primary archetypes that the dreamy ditz might work with, the serious scientist and the nondescript main are on the entirely opposite end of the spectrum.
Her dialogue is also incredibly stupid. She continuously states the obvious, is absent minded for major events, and is far too immature to be credible as an experienced professional (I keep reiterating this point, but it's very important).
Had Shion been in a more minor role and profession, she might be tolerable. Make her a highschool girl who gets caught up in the chaos, or a love interest to the actual protagonist -- these would have been fine. She might even work as an intern assistant to a scientist, whose bumbling is a bit of comic relief or serves to create a cute balance for her more straight-arrow mentor.
As that straight-laced scientist and consummate professional? As the person out to save the universe? Shion sucks.
You really go back and forth there.
Here's all I have to say. I really, not for a moment, found that I was annoyed, or that I even cared one bit, about the perceived "problems" you have with Shion.
She's not a great character. In essence, she's a nobody protagonist. Like a silent protagonist, except she does actually talk. She's important for a few reasons, mostly involving the role her parents played, and the fact that at some point she hopped in the sack with Kevin, the real brains behind the operation.
Shion being a not-so-amazing protagonist in no way decreased my enjoyment of the game. I think you have to force yourself to care as much as Mark does to get this upset. :)
That's a lot of *words* to state that she's a typical one dimensional anime heroine with stupidly thick plotarmor.
The only reason why she was the main character to begin with was that KOS-MOS wasn't cliched enough for the role (though, in reality, KOS-MOS really was the main character of Xenosaga while Shion was just the bumbling sidekick who simply had narrative prerogative).