Assuming the Yin Seal takes actual effort to make (it must, otherwise why couldn't Shizune do it?) The that means Sakura basically had a jutsu active for 3 years to create the seal. That would be her handicap, though a small one. However, she said it was a benefit that she didn't have to divert any chakra to keep a henge jutsu going like Tsunade does. So, I guess relatively minor jutsu can have an effect on chakra capacity.
Other than that, Kishi just seems to dislike women in general. The guys always look cool and are defeated in cool ways even when beaten. On the other hand, Konan was killed with a metal pipe, he drew Karin get taken out by a single kick from Danzo, he drew Sakura getting hit in the face with a rock in the background of the war, and he drew Hinata falling flat on her face while trying to run after Naruto. He put in actual effort to make females look bad. So, Sakura should get bonus points just because the author is biased.
On paper, she seems fine to me. Kishi just decides to make her look bad, probably because he thinks she is bad.
Same way he just decided not to spend any time on the Byakugan at any point in Shippuden and then just threw it back in as an after-thought when he was whoring out the franchise with Kaguya and the Otsutsuki. Even after doing that, he gives the Otsutsuki aliens the Byakugan as if he's trying to make up for ignoring it, but then never has them use it to do anything. At all. They might as well just not have it.
He tries to make up for some of his shortcomings in the story to please fans, but half-asses it and just makes contradictory situations where one scene makes someone/something look really cool and then another scene makes it look stupidly useless or incompetent.