I've always seen the VFs as the fast and agile units and the MS as the tanks, and I still think a VF vs MS fight would be fairly even with VFs holding the agility edge and MSs packing the armor and firepower. I'm sure some MSs would be able to hold their own with a VF in terms of mobility, put manuvering thrusters in the right places on the limbs, like the GP01fb and it could prove to be fairly agile. And really aside from the 100mm machine guns what MS weapon can a VF take mulitple hits from? A buster rifle? The Agni Cannon? The Dober Gun? Wouldn't a direct full blast shot from a double buster rifle, Mega Cannon, Satelite Cannon, or some other "anti-colony" weapon overload a pin point barrier? And some of those big guns have a pretty decent rate of fire. I'm still not convinced the standard gunpod and micro missiles would do much against Phase Shift armor.
Since they're both Kawamori's creations I'd like to see a match between the GP01fb and a VF-1S Strike, with no nukes.