Graph problems with good characterization but not known to be in $P$
In one of my blog posts, I mentioned four problems (Factoring, Parity Games, Stochastic Games, A Lattice Problem) that are known to be in $NP \cap coNP$ but not known to be in $P$.

Parity Games and Stochastic Games can be considered as "graph problems".

Also, The Two Bicliques Problem is in $NP \cap coNP$. This is a natural graph problem that is not known to be in $P$.