The hybrid spec is actually pretty awesome in PVE. The problem is managing heat and 3 dots as well as Proto Flamethrower and PPA. If you can keep full dot uptime and use triple stacked flamethrowers on cooldown you'll be not only competing with Snipers and Mara's but also putting them to shame. That said though it takes a lot of practise and without the UI mods games like WoW has it becomes easily the hardest spec/class to play properly.
The "good" PT players can still hit big numbers in raids it just gone from 3 button dps to 6.
I will agree though that the burst has completely gone from the PT class as it now takes me twice as long to kill the Anomalies in the HM Terror from Beyond fight.
Finally, this does affect PVP more since its all about burst and randomly hitting buttons as opposed to trying to sustain high dmg for a long period like PVE.