I look at the Bacara and TE Gunner's thing as a Pauldron... Seems like the Clones just had a variety of them (as far as their "look" or physical construction)... Why that is, I'm totally clueless. Maybe the Clones made them on their own by their specific legions, but the Empire stripped them down to a specific uniformed style for all troopers with the colors meaning the same across the board.
At least that's how I'm looking at things right now.
On the "skirt", I think it's more means of a Commander establishing himself as unique among his men, and perhaps paying some tribute to the Republic's most elite Clones too... I dunno. I wouldn't think it would hinder movement or be a "problem" for troops and movement.