Certain armor, to me, would be "special" because of necessity... Underwater Clones for instance would require training a basic Clone couldn't acheive... Aquatic legions would just be a necessity to train separately. To me though, these are fewer in number...
This is a beef I've had with the OT "Troopers" for years now... Sandtroopers aren't "Sandtroopers". They're Stormtroopers in their field gear. At least to me that's how I view them. The Pauldrons, the modular packs that seem designed to swap out parts for different needs, are what the basic Stormtrooper wears... No special training needed. Same with the "Spacetroopers" we see outside the Death Star... They're Stormtroopers, just using the zero-g capabilities of their armor. Zero-G training is something a regular Trooper could easily receive...
Now the elite Spacetrooper legions are, to me, a limited special group... Like Navy SEALS in space. They have training far beyond the basic Zero-G training a Stormtrooper goes through.
Likewise, "Snowtroopers", are just Stormtroopers in their coldweather armor to me.
I agree on the "specialized Clones" issue though... Too many. I like the Flamethrower Clones, but why are they sporting the special armor? What's the point?
I'm looking at a lot of the armor as just things available for Clones, and some batallions adopt them and some don't. There are far too many, "Special" legions of Clones though, for my tastes. It gets corny, and becomes more and more a sales ploy and less and less a logical reason for armor differences I think.