I've played a Smuggler while a friend of mine has played a Trooper alongside me for every single class story cut scene (except those on our ships) from level 1-45, and the Trooper story was consistently the better one on each planet.
I believe the Smuggler has the best ship reveal, but that's the only thing that really stands out. Case in point, Light and Dark Side choices. Smuggler Light Side is Han Solo coming back to help Luke destroy the Death Star. Smuggler Dark Side is just a faster version of Greedo, slimy. These are pretty cut and dry, and get boring. Trooper Light Side is a good soldier defying his superiors and colleagues while they squash rights and freedoms. Trooper Dark Side is a downright crusade against traitors. Much more dynamic than the smuggler.
I enjoy the Consular a lot, but I'm a huge Jedi story fan, so I'm biased.