Thank you for asking this question! To start off with, some of your questions are already answered in our FAQ. There are no humanizations, and we allow canon AUs. That said, we will also allow CRAUs, but not fanmade AUs of characters, so thank you for helping us to spot this hole in our FAQ.

MMO protagonists are allowed, as the faq says, and yes, multiples are allowed.

As for cases like Shepard, we've decided that we'd allow both female Shepard and male Shepard to be apped separately, but not to include multiple versions of them.