Given a new problem in $\mathsf{NP}$ whose true complexity is somewhere between $\mathsf{P}$ and being NP-complete, there are two methods that I know of that might be used to prove that resolving this is difficult:
- Show that the problem is GI-complete (GI = Graph Isomorphism)
- Show that the problem is in $\mathsf{co-AM}$. By known results, such a result implies that if the problem is NP-complete, then PH collapses to the second level. For example, the famous protocol for Graph Nonisomorphism does exactly this.
Are there any other methods (maybe with different "strengths of belief") that have been used ? For any answer, an example of where it has actually been used is required: obviously there are many ways one might try to show this, but examples make the argument more convincing.