Female characters are generally scrutinized much more than male characters. It is a sad fact that is prevelant in pretty much any fandom nowadays.
Take a series like Naruto for example. In it, we are told a whole lot about the titular character Naruto (his background, his goals and motivations) and how he gradually is able to overcome most of his weaknesses and grow as a character, not only in terms of strength but also in terms of personality. The same thing goes for the other male lead, Sasuke, although his story takes a signicantly darker turn towards the end of part one.
Meanwhile, Sakura spends most of part 1 being generally overshadowed by her two male counterparts. However by the end of part one, it is pretty clear that she has indeed gone through a significant development, not so much in terms of strength (this is mostly evident by the fact that unlike pretty much every other character in the series, including other female characters, she has no unique powers or bloodline techniques or really just special traits at all) but more in terms of personlity. In short, she went from a slighty egotistical brat to a very compassionate person who cares a lot about her friends and those close to her and who would do anything to ensure their safety and thus part one ends with her seeking out one of the strongest female ninjas of all time in order to train to become stronger.
This is what I, and most other Sakura fans, like so much about her. Sure she's not the strongest character ever and her background could be a bit more fleshed out, but what she lacks in those two areas, she more than makes up for in terms of just being an interesting character. Still, a lot of people didn't take kindly to her. They said that she was a *****, that she was boring and uninteresting and that she was useless and weak.
This leaves us at the start of part two, which takes place two and a half years after part one. Now, after having spent the last two years training relentlessly, she has suddenly gained a considerable oomph in terms of strength. Not only does she now has super human strength which makes her capable of demolishing solid rock with her bare fists, she has also become a magnificient medic, so much in fact that many consider her to be a medical prodigy, though that is strictly a fanon thing. She is never directly referred to as such in canon. Also, in terms of personality, she is now much more mature and focused on her duty as a ninja and overall she is just a much more pleasant person.
So what happens? Well, now she same people who complained about her having a million flaws and not being too weak instead complains about her being, you guessed it...A mary sue!
So in the end, what it all comes down to is this: Females never win! :-/