- The pizza wasn't quite up there with the rest.
To me, this is completely natural, assuming that it's already clear from context what "the rest" means - I assume you're referring to the rest of the food at a restaurant.
- The pizza wasn't quite on par with the rest.
This is also completely natural (with the same assumption as the above), although to me, it doesn't imply as strongly that the rest of the food was "up there," i.e., really good. It just means the pizza wasn't as good as the rest. "On par" suggests that the rest of the food was probably at least decent.
- The pizza left something to be desired.
Also totally natural. It means the pizza wasn't very good. Unlike the other two, it obviously says nothing about the rest of the food or how the pizza compares to it.