longeyes,
Good question! I would say it depends on what kind of SHTF situation you have in mind.
If it were for laying low and hunting, I would say the Marlin. It looks more benign, has a lower noise signature, and will take medium game out to 100 yards quite well. Also, you can remove the buttstock with one screw and have a gun that will easily fit in a backpack.
If repelling hostiles was the job at hand, I would definately take the Mini. More firepower and MUCH easier to reload. If you have good magazines (PMI is the only aftermarket mag that I would bet my life on.), the Mini is rock solid reliable. I would get a slip-on flash hider and a synthetic stock (maybe a folder) to put on when the SHTF. If that happens, who cares if it's legal or not? If you do, make sure that you test sight in with them on the gun. I would also look for a more sturdy rear sight, as I think the stock sight is the weakest link (besides the accuracy when the barrel heats up) on the Mini. Also, Cheaper Than Dirt sells stripper clip guides for the Mini that allow you to use M-16 stripper clips to refill your mags. I have some, and they work quite well.
If these were my only two choices, I would probably get both. They complement each other quite well and neither is so heavy that you couldn't carry both if you have a large backpack. Just my $.02 worth.
David
PS - I do own both rifles.