Best reply so far lol.
Any way, to OP.
Level to 50, then come back and talk about it. This is an MMO, which traditionally has a progression of both skills and gear. If that's not what you're expecting, you're playing the wrong game.
To answer some of your other statements, Kotor 1 (or maybe earlier, it's only the first time I heard of it) introduced the Cortosis Weave. It was a strange force and lightsaber resistant material, and most non-jedi are assumed to be wearing it.
Troopers and Agents are both highly trained, and during this era that training includes vs. Force Users. I may be incorrect, but the Trooper's played by Players are suppose to be the best of the best, Akin to or even better than the ARC Troopers of the movies. If this weren't an MMO where anyone can roll a trooper, you literally see maybe 50 or so troopers actually skilled enough to best a Jedi/Sith.
Bounty Hunters are I guess assumed to be battle hardened, and the one played by the character is once again exceptional, adept at fighting force users as much as trained commandos.
The only class I have a hard time justifying via Lore is the smuggler... to which I reply "Try and kick me... see if you get that leg back."
I'm sure someone could find a justification lore wise for smugglers, but I just don't like them.