A fly on that wall?
Aye - but me woolies are sprayed with permethrin!
I guess for me, the thermal concerns of an enclosed crotch far outweigh the specter of mossies. Now don't get me wrong, should the sky be moving ahead of me, I will don the softshells which are also treated, but in hot, summer conditions the Kilt wins out.
I have tried the Columbia shorts, pants, and convertibles - found them to be the best in all honesty. The REI Shara convertibles? For me they are like being wrapped up in saran wrap - no breathability, little in the way of a comfortable cut and really not that durable. The Ex-Officio Amphis are really nice too - maybe even better than the Columbia's, but the cut was all wrong for me. The belt was uncomfortable under a pack.
As for running shorts, they work in cooler conditions admirably, but lack the pockets sought by the OP. As do the running pants, as the OP pointed out.
But yes, I can see why one might balk at the idea of hiking through mossie infested lands with a kilt on.