I totally feel the same way. I switched from an Emp heavy server to a Repub one to play with friends. Loved my operative, so I thought "I'll roll a scoundrel!" - mirror class, right?
It just didn't feel right playing even though they have the exact same ability sets. It felt clunky and unnatural, and I couldn't put my finger on it because they were the exact same class! Then I realized it was completely the aesthetics like the OP suggests. Operative has a blaster rifle, aiming and sniping at range then when closing whips out a flurry of knife attacks, spinning every which way... throw a grenade or two... fun class to play!
Scoundrel doesn't seem like it knows what it is doing.... pulls out scatter gun here or there, nuts to the crotch, pistol whip... I guess that fits the "feel" of a smuggler because you are graphically pulling out everything but the kitchen sink to survive a fight. Also blaster pistols are so tiny and graphically under-represented that you don't really feel your upgrades imo. I really wish I could use a rifle :/
At the end of the day, they are all the same (although it could just be me, but scoundrel animations seem a lot slower than operative), and I recognize that it is all just in my head. I just have never experienced such a complete 180 in play enjoyment between two mirror classes.