The one thing that can really make a figure rare is a variation. It can be the figure or the card itself. The Orange carded Boba Fett and the paint variation on his hand is an example of figure variation. It's one I couldn't care less about but some variation hunters went nuts over it. An example of a card variation can be found in the orange carded Ben Kenobi with the spelling mistake in the character bio and the picture change. I've got the rarer version only because it was the figure I happened to pick up when I went on a toy run that day. I wasn't looking for that variation I just stumbled upon it and I still don't care that much about it.
Variations can make a figure rare, but only to certain collectors. And even these "variations" can be found in great numbers, there are thousands of them out there.