Well, I also suspected they'd go with it, but there still was an element of uncertainty, after all, the movie's based on the game very loosely (at that point we already knew about the Galactic Rangers, Nefarious, completely different Ratchet with different goals and motivations, completely different Drek, etc.), so I wouldn't be shocked if Qwark's betrayal concept turned out to be scrapped in the end. Also, we didn't know how EXACTLY would it go - the trailer made it pretty clear that Qwark turns to the 'dark side' after he gets jelaous about Ratchet's successes, not like in the original game, where he's been working for the enemy from the start. It's not a big shock, but I still wish they kept it for the game/movie.
Well, since I'm a quite fresh fan and usually watch gameplay videos and open the R&C wiki to get information about the previous games, I'd say it was Cronk & Zephyr's death. Ratchet's "death" may have shocked me, but I felt relieved when Clank altered the timeline and thus saving Ratchet. But Cronk and Zephyr, those guys were a perfect duo like Ratchet & Clank, and both of them got killed at the same time. And when Ratchet looked at them for the last time during the slow-mo scene, you knew that Ratchet, with his own eyes, saw his friends getting killed. But hey, at least they returned as ghosts.
Even though the Thruster-pack gave me better mobility, I would still pick the heli-pack as my favorite. I think the heli-pack is just a very iconic upgrade for Clank. Maybe because it has appeared in many games and I'm used to it.