In the store, obviously, all figures are "worth" the same. The harder to find ones can sell for more on the secondary market, so they are probably more valuable in terms of re-sale value or if you can't find them in the stores yourself.
I was amazed to find a green commander a couple weeks ago, given how impossible it is to find anything good in my area with the large number of collectors (and scalpers) here. But I saw a few more green guys a short while later, which leads me to agree with the above assessment that, yeah, they are becoming easier to find and therefore "cheaper".
But, as Chewie said, they're YOUR figures now, enjoy them however you wish! I recently pillaged some rare (and expensive) old EU figures for customs 'cause, what the heck? I wanted to and it was fun.