It's hard to know what they're thinking. Both players were drafted by the Sharks and both of their families are heavily rooted in the area, so you can't really say Marleau will definitely stay but Pavelski won't. Both Pavelski and Marleau would probably be unhappy playing on the 3rd line as well, and both of them may or may not complain to the coaches. However, Marleau already has public prior history with not getting along with a coach, Pavelski doesn't.
Honestly, no Top-6 will like to play on the 3rd line, but I don't think Pavelski would dislike it and complain anymore than Marleau would.
EDIT: FTR, I'm not saying Marleau is more likely to complain either. Both of them love it in San Jose, and I don't think either of them would make a big deal about it. I like to think that both of them care more about winning than about their stats. I could definitely see Clowe complaining though.