Level 30 something Scoundrel here and I'll throw in my 2 cents. I used Scrapper up until Balmorra, and then switched to SawBones. From my experience, Scrapper is a bit harder to stay alive, but you mow down mobs quicker while the Sawbones is easy to stay alive but it takes awhile to progress through mobs due to your companion's damage not being too high (at least with Corso and Bowdaar with green gear).
PhazAeth
Edit: Rotation for Scrapper (General PvE Situations)
Stealth
Apply CC (after level 20 for non-robotic) to Strong/Elite.
Set my companion on a mob (usually the "stronger" or healer of the normal mobs)
Use backblast on the weakest mob to hopefully 1HKO them.
Then pistol whipped the next strongest.
Applied Pugnacity
Quick Shoot until dead.
Move on to next mob opening with Backblast.
Pistol Whip
Etc...
I use Upper Hand Abilities, Grenades and interrupts liberally when they are available and as needed. You'll get the feel for it as you level up. Pistol whip and back blast are the bread and butter. Grenades will break CC, but it can also serve as a quick knockdown on a non-strong NPC. It's free to respec once a week, so give it a shot and if you don't like the play style, head back to the Republic Fleet and change specs.
Hopefully this helps some.