It's the same average damage, so it's only a minor variation, just like the "difference" between Commandos using an Assault Cannon and Mercs using 2 pistols or a Jedi/Sith using a Vibroblade rather than a Lightsaber. It's not a difference since they're going to average out to be identical.
How about energy management?
I've got both a PT and a VG.
I went on my ship and decided to use the warzone training dummy to test this theory out.
On my vanguard, I spammed Ion Pulse until I ran out of ammo. I got 8 shots in.
On my powertech, I spammed Flame Burst until I ran out of energy. I got 9 shots in.
I repeated this test 4 more times, and only a single time, did the powertech get 8 shots instead of 9.
The difference is minimal in real time, but statistically speaking, powertechs have better energy management.