Completely agree that size is not a good proxy for estimating MIP difficulties. Internally we colllected a bunch of very hard problems to sovle from different domains. Some are actually pretty small, say a few thousand variables/constraints. IMHO what made hard problems difficult to solve is actually the 'intneral structure' of the problems. And modern industry solvers all have a lot of built-in heurstics to take advantages of the structures, i.e., what kind of cuts, presolve/diving/branching strategy to apply, how to get the bounds ASAP.
Interestinglly at some point some folks even tried using machine learning to predict strategies. Didn't work quite well back then (10+ years ago). There was some work of using seq2seq for MIP (pointer network, I think) a few years ago; worked OK. So I'm really looking forward to some breakthroughs by LLM.
It's a shame that after IBM aquired ILOG (which owns CPLEX), most of the ppl left for Gurobi.