I believe it is dependent on how you will use it. As far as resale value, and popularity, the 3100 (1/2 ton) will, in the opinion of most, be more collectible. It is just a little cleaner, and sporty, if you can apply that to older trucks as it was a light duty, town crusier. If nothing else, it has been beat into peoples heads for decades that the 1/2 ton is "cooler" so their value is better in terms of vehicle peer pressure!
3600 is just a little more beefy, 3/4 ton, usually 8 lug wheels and intended for a little heavier work. It is less likely that you will find optional deluxe packages, 5 window etc in the 3600 series as their purpose of origin was more focused on work, although there are many out there that do have these options. If your needs require hauling a little more weight then most certainly this is the way to go.
Basically the answer is yes the 3100 is a little more desirable. It is along the lines of 2 door vs. 4 door in the car realm but not as drastic. But ultimately, "if you like it, go for it!." When the right truck calls, it is difficult to say no, and most likely you aren't going to re- sell it any time soon. You might even get a better deal on it as a 3600 so the resale value thing might work in your advantage.
