I never really thought of Chiaki as a Mary Sue. I mean, she's obviously meant to be a sympathetic character in DR2 already, she's obviously set up as "best waifu", much more than any single girl in DR1 (where for me Kyoko and Hina were on par really)
. But this is Danganronpa, ALL characters are exaggerated and usually defined by being able to do one/two things very well. More than proper flaws, a lot of characters simply have quirks. Chiaki is certainly supposed to be attractive for the combination of sweetness/innocence and for her gaming hobby (which obviously hits a chord if you're, well, PLAYING DR2). But she's also portrayed as very shy - also lethargic - and in DR2 in the end her supposed "perfection" isn't even that inexplicable given that she's not even human. Here her role was certainly a bit weird - going from loner to heart and soul of the class - but it's hard to consider her a Mary Sue for it when we knew from the very beginning that she was due for some horrible death, or worse.
Also, let's face it, if there's a Mary Sue in this story it's freakin' Junko Enoshima
. Just... is there a word for a Mary Sue that is actually evil and a villain and her super-convenient perfect talents are all in service of making life miserable for everyone else
?