Natural NP-complete problems with "large" witnesses
How about the edge coloring number in a dense graph (aka Chromatic index)? You are given the adjacency matrix of an $n$ vertex graph ($n^2$ bit input), but the natural witness describing the coloring has size $n^2\log n$. Of course, there might be shorter proofs for class 1 graphs in Vizing's theorem.

See also this possibly related question