Trinity was bypassable, but the infiltration where you go onboard a boat to place bombs in the cargo was bugged for 7 days alone while i waited for it to be unbugged, then i stopped playing the game altogether. It was brought to their attention atleast a dozen of times and so was the trinity quest.
Apart from that, the story was completely broken and in the later levels, introduced characters i've never seen or heard of in the story line.
Spoiler ahead:
Like the Norm who's trapped and you have to kill. Who is it? Why have i not heard about her?
The cyborg/spider wannabe whatever it is, who talks with a sorta russian accent who you go underwater into the caves with. The game tells us i've meet her before because they interract by telling eachother how good it is to see eachother.
I was playing with my girlfriend who played GW1 and i asked her who those people were, since it could be tied with the previous installment. She had absolutely no clue who these people were.
I SUSPECT that they removed parts of the storyline because they were bugged and a bandaid solution was to make a big gap between the storyquests, or it could be that the different paths of the quests are just that badly designed.