How does the piston area in those 2 pot calipers compare with the original single pot?
If the piston area is greater, then it will give you more braking effort for a given pedal pressure, so it's bound to feel like an upgrade.
The problem is, you'll have shifted the brake balance towards the front axle since you haven't also increased the piston area at the rear axle. This means the (standard) front disks are now getting more punishment than before, since they are doing a greater proportion of the braking, making brake fade more likely. It will also affect the car's handling under braking and perhaps worsen the overall stopping power. If the piston area is the same, then no problem of course.
Either way, all you've actually "upgraded" is the life of the pads, since the pad area is now greater.
The only way to cure brake fade is to upgrade the part of the system that dissipates the heat - the disk.