The general intuition here: it's easy to prove a graph contains an N-clique: just show me the clique. It's hard to prove a graph that doesn't have an N-clique in fact doesn't have an N-clique. What property of the graph are you going to exploit to do that?
Sure, for some families of graphs you can -- for example, graphs with sufficiently few edges can't possibly have such a clique. It's entirely possible that all graphs can have similar proofs built around them, although it'd be surprising -- almost as surprising as P=NP.
This is why the complement of languages in NP are not, in general, obviously in NP -- in fact, we have the term "co-NP" (as in "the complement is in NP") to refer to languages like !CLIQUE.
One common approach to make progress in complexity theory, where we haven't made progress against the hard questions, is to show that some specific hard-to-prove result would imply something surprising. Showing that NP=co-NP is a common target of these proofs -- for example, any hard problem in both NP and co-NP probably isn't complete for either, because if it were it is complete for both and thus both are equal, so somehow you have those crazy general graph proofs.
This even generalizes -- you can start talking about what happens if your NTMs (or certificate checkers) have an oracle for an NP complete language like CLIQUE. Obviously both CLIQUE and !CLIQUE is in P^CLIQUE, but now there are (probably) new languages in NP^CLIQUE and co-NP^CLIQUE, and you can keep going further until you have an entire hierarchy of complexity classes -- the "polynomial hierarchy". This hierarchy intuitively goes on forever, but may well collapse at some point or even not exist at all (if P=NP).
The polynomial hierarchy makes this general argument technique more powerful -- showing that some result would make the polynomial hierarchy collapse to the 2nd or 3rd level would make that result pretty surprising. Even showing it collapses at all would be somewhat surprising.