Neither tree has been particularly great for PvP, but you can be equally effective with either. The only people saying assault is the defacto PvP tree are those who couldn't get gunnery to work for them (and had never seen an effective gunnery commando).
They both have their strengths and weaknesses in warzones, and both needed improvements.
There isn't an effective gunnery commando, any elite commando dps can easily be replaced for the better, by an average vanguard. And an assault commando is a poor mans assault vanguard. I call them commandos with buyers remorse, or people who are smart enough to know they ****ed up but dumb enough to stick around on the class wasting their time.