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.)
Yeah, that would be my guess. Crystal Pepsi tastes noticeably different than regular, and caramel color is used in such small qtys that it is considered borderline flavorless.
If you look at popular grapefruit sodas Fresca is clear, but Squirt is cloudy because Fresca uses water soluble flavors and Squirt uses oils. (Squirt is the better product by far IMO because a lot of the grapefruit flavor is from the oil in the peel.)
It’s always possible the geniuses at the flavor houses Pepsi buys from have some magic I don’t know about though. But I’ve never heard of any way to make emulsified oils clear, since they refract light differently.