In Superman/Batman: Apocalypse, it's shown that Supergirl's cellular structure is much more dense than Superman and that Supergirl is supposed to be much more powerful.
Why is it then that she gets hurt much easier than Superman and she's not as quick or strong?
Although Batman says her celluar structure is a "shade" denser and that "she metabolizes sunlight more efficiently," Superman has been on Earth for many years, whereas she has only just arrived. She hasn't had as much time to absorb radition from Earth's yellow sun as Superman has.
Batman also says "bottom line, she might be more powerful than you"+
There is no guarantee that she is or will be.
+Emphasis added
Two likely possibilities haven't been mentioned yet:
Kryptonian strength is usually described in relation to human equivalents (that is, Superman isn't terribly "super" among his own people). Even if Kara's physiology metabolizes sunlight more efficiently than Clark's, she's still substantially smaller and less muscular than he is, so she might still end up being weaker.
If I'm getting a 200% boost to a natural strength of 10, and you're getting a 300% boost to a natural strength of 3, I'm still ultimately going to be stronger than you.
I know plenty of 90-pound girls who can take a punch to the gut without flinching, and I know plenty of body-builders who cry when they get poked with a syringe.
Kara is Kryptonian, so she's "tough" in the sense that it takes a lot of force to damage her biological tissues, but mentally and behaviorally she's still a normal, teenaged girl. By contrast, Clark grew up working on a farm, and has spent years (decades?) fighting and pummeling incredibly tough opponents in one-on-one combat.
It could be that Kara is stronger and tougher than Superman statistically, but her inexperience and lack of combat training prevent her from being as effective in a fight.
I think that she is younger than Superman. She will be as strong as him when she reaches the same age.
