I know exactly what problem your describing.

Over the years, I've discovered that it's really easy if you push in the piston before removing the caliper.

With the caliper still bolted in place, I use a long-handled, large pair of slip-lock pliers spanning the ears (the "loops" that the pins pass through) and caliper body to just nudge the pads away from the rotor, leaving a little gap on each side of the rotor. Then I take a couple of long screwdrivers and push them into each of the spaces and pry the pads back toward the caliper, forcing the pistons inward. The pair of screwdrivers are pried back, crossing each other as you pry back the pads.

It's best if you can use two screwdrivers at the same time, because as you push on only one side, the opposite piston tends to push out again slightly (although you can do this eventually if you keeping trying, each side, one at a time).

I'm just using the outermost edge of the rotor as a fulcrum, so it doesn't leave any marks at all on the rotor surface. But with this method I can force the pads, and therefore the pistons underneath, fully home with ease.

However, to do this the caliper has to be bolted in place, because I'm using the screwdriver against the piston, which in effect is against the body of the caliper, so the caliper must be held securely in place. You cannot hope to do this with the caliper dangling on a wire because it can swing and move.

Hope this helped.