Phase 2 Troopers don't bug me. It's the phase 1 versions that look like walking, dessicated corpses as they run up to you that freak me out.
Most of them are blaster-proof; they're ray-shielded, so you'll have to rely on heavier weapons. The Conc rifle works well as long as you keep your distance, as do grenades and mines (drop mines as you run away, but be careful to not walk into your own ordnance
I got past them by relying on the cheat code LAREDLIGHT, it disables the AI and lets you seek shelter/attack while the enemies are frozen. A slightly fairer way to do it is to freeze them, then "test-fire" every weapon you have at them, listening to the SFX to see which does more damage. Then you can pick a weapon, put some distance between you and it to give you a fighting chance, and unfreeze it.
For Phase 2s, use your captured plasma cannon, but remember that the rockets are much too slow to hit a DT. And of course, perfect you grenade and mine technique.