I think most people would suggest that the normal scattergun is better than the FAN, and normal wrench maybe better than southern hospitality due to more damage (maybe, I forget if there is a no-crit effect or something) and getting toasted by pyros if any are around.
The ubersaw, axetinguisher, and equalizer are pretty much pure upgrades to the original weapons. The tomislav is good but I switch to the minigun sometimes since the nerf when I actually need to do better damage.
So, you're left with 3-4 weapons that are purely better than the new weapons...notice how the other poster said "90%", not "100%"?
I don't have the math for the total number of weapons, but if say, 6 new weapons are better than the vanilla version, there could still be 54 other non-vanilla weapons that aren't better, and the 90% figure would still be correct.