this is definitely NOT guess work.
i've spent about 12+ hours and 2-3 million (mod swapping) testing both Merc/Pyro and VG/Assasult, multiple specs.
TORParse breaks down everything. that's not saying i have the best rotation for the class/spec, but i do what i would do in actual combat. i'm sure there is some room for improvement.
I don't think the original poster was discussing the Merc (Pyro) spec, but rather the Merc (Arsenal) spec, vs Powertech. Merc/Arsenal is better damage than Merc/Pyro, which is why I don't think your post is really in tune with what the thread is about.
Powertech (Pyro) definitely has better damage output than Arsenal. I haven't tried Advanced Prototype, but I've read up on it a fair bit. Apparently, while it doesn't match the dps of Powertech Pyro, it still does better than Merc (either spec). While Advanced Prototype also has some nice utility, it lacks the mobility of Pyro due to the need to remain stationary during flamethrowers, which are a part of its rotation. It is also easier to manage in terms of heat, since it automatically decreases heat at an increased rate.