I liked Factions' PvE, but as has been said, it didn't feel as well done as Prophecies. This isn't simply because the map is so much smaller and thus takes less time to explore (I can still see some beautiful sights in Cantha), but that the storyline of Factions didn't satisfy me.
I didn't expect it to be as expansive as Prophecies, but I did expect it to be better than what it turned out to be. On the other hand, storylines in so-called RPGs these days usually leave much to be desired, so... *shrug*
In the scheme of things, PvE in Factions is fine. I'm having a hard time finding the motivation to pull each of my characters through the multitude of quests/missions for elite capping, but then, the third and fourth time through Tyria got tedious as well.

Guild Wars is about doing stuff (whether PvP or PvE) with your friends. Really, no matter what you're doing, if you're in good company you're more likely to have fun.
