Oh yeah, I definitely know she was seen as a Mary Sue in the beginning, which only made it really hilarious when it was revealed they named her Mary Sue Poots at the orphanage
I think that was a pretty deliberate move from the writers though, just like they made Ward seem like Joe Normal for a big portion of S1, people complained about how he was whitebread and boring and then bam, that big reveal. With Skye her transformation was a bit more subtle, but I do think it was deliberate that they showed her as a somewhat predictable character at first only to quickly break her out of that role.