To answer the question of why these Creatu didn't get dye colors in the first place.. Pretty much, other than gold, dye colors didn't exist back then. P: I'm pretty sure even when the three were retired, new dyes were still being released. Heck, amber didn't come out and finish off the dyes 'til.. what, almost a year after that?
Anyway. I agree that by not having all the dye colors, the retired trio retains an extra air of specialness and rarity. I.. have always been partial to the idea of Credit Shop pets coming in just a few special colors, really. Even if I have gotten used to the new ones having dye colors, I sure raged when it was first announced. xD
Besides, unless you already have eight or nine spare naturals of one of these species lying around, it'd become even more impossible to get a full collection than it is now, with how much all of 'em would cost. Dye kits were created to give extra value to natural pets. I'm not sure the retired ones exactly need that, since being retired has pretty much already accomplished the same thing to a huge degree. They've got like. All the value, man.