I agree with DH about a well sorted mk3 being better then a mk2, as it will be stiffer overall. Also, as far as I know vw used thinner steel for the mk3 shell to save money and because the shells were galvanized, so better protection. They rust easily because of the thinner shell though.
I agreed that of the box the mk2 will be better.
Not wishing to dampen your bonfire fella but the MK3 used the same thickness steel as the MK2 but there was just more of it. Addtionally, the MK3 Golf did not have a galvernised body until 1994- and if it's galved, it won't rust at all unless the galv is scratched or damaged.
Other than that the chassis is a slight improvement over the MK2 but too overweight and under-powered to use it. When first developed the MK3 16V had 177hp and the VR6 was supercharged and ran 220hp approx but due to poor economic climate and rising insurance costs and two cars that would be competing with each other VW de-tuned them both so the 16V became the 150hp we know today and the VR6 lost it's supercharger.
out of the two? I'd have a MK2 everytime.