Is there such a thing as starting with a weak kind of set theory and making an argument to show that it should be expanded into a stronger set theory such as ZFC? Something similar to going from the rationals to the reals? With number systems, we have evidence which forces us into a stronger system (sqrt of 2). Is there such evidence with set theory?
I mentioned the real numbers because in that situation there is obviously something missing. Is there obviously something missing from "weak" set theories? My interest is: to what extent can we justify the axioms of infinity and choice? Is there a higher level principle (of the "there is something missing" sort) which implies infinity and choice should be part of our system?
For category theory, sometimes you could need to handle the set of all sets and this set does not exist in $ZF$. But using $NBG$, you can speak of the class of all sets which would be similar to the set of all sets but untouched by the same problems that arise when you speak about the same concept in $ZF$. So $NBG$ possess a larger ontology than $ZF$ and indeed, $ZF$ can be constructed as a subsystem of $NBG$. I'm just not sure if this is the kind of completing you're looking for, but if this is, take a look at the first chapter of Goldblatt's: The categorial analysis of logic.
I guess that these theories can be completed by generating a new theory in which certain sets that were not accepted in the previous theories exist for the new ones, just as the set I mentioned before. Take $ZF$ and remove the axiom of the power set, it will be a less complete theory, that is: You won't be able to construct certain sets that could be built with $ZF$.
This reminds me of an exercise in the beginning or Jech/Hrbáček's: Introduction to Set Theory They give the axioms of existence, extensionality and comprehension. A little later in the book, they ask you to prove that with these axioms alone, you can only construct $\emptyset$.
Start reading what I suggested, soon Asaf will emerge from the darkness and settle this down.