The OP said (in the last paragraph) that the ingredients that go into colas are the kind that make the drink cloudy. Crystal Pepsi was clear, even without the coloring.

Presumably it's because they changed to use flavors that are completely water-soluble. That would explain a difference in taste.

(I know they tasted different with my eyes open, but I never did a blind taste test between the two. It would be interesting to know how close they really got to the original flavor.)