The difficulty curve is all wrong. You spend at least 12 levels on a 'tutorial island' with little or no challenge. Then you hit one extremely difficult mission city, and are then sent to Cantha to fight against nothing but level 20s. It's like there is a complete absence of mobs between levels 14 and 20 in the game. Fighting things like that, you'll get to level 20 very quickly...leaving the later 3/4ths of the campaign utterly meaningless, as your level is maxed soon after leaving the 'tutorial'. I understand the game is geared towards PvP, but if you're going to *have* a PvE campaign you might as well give the players *some* incentive to finish it.
Oh, there's one challenging mission on Shing Jae -- Captured Son, which you can get at 10th level and which will kick your face in. This mission is equivalent in reward and difficulty to The Villany of Galrath. Why would you allow 10th level characters to attempt it? I could also mention the mission on Cantha you'll get at 16th level that gives you a -3 Health degen before sending you up against level 24 opponents...but that one I'll mark down to pure developer sadism.
Then there's the character classes. The ritualist is interesting, but only as a main class, as so many skills depend upon communing and that depends upon spawning power. A secondary ritualist seems doomed to either casting weapon spells or being a weaker elementalist. The Assassin, on the other hand, is the full package -- interesting utility, some great (if energy inefficient) spike damage, and a role that we haven't had before, that of the quick and lightly armored melee combatant. And what do lightly armored melee fear the most in these games? How about enemies that explode upon death, which by chance happens to be the defining ability of the main quest's main enemies. The Factions campaign seems engineered specifically to neuter Assassins into irrelevance. I'm tempted to bring my assassin to do the Prophecy campaign, where I think the class would be much more useful.
I could go on. About the maps (let's take something that the players rely upon, and make it useless by using confusing, maze-like map design everywhere), the missions (no skill rewards, ever?), and the loot drops (what, are there sixteen different varieties of 'diseased flesh'? How about something I can salvage into cloth, which all the Faction armors require?). But I think the point is made. Factions, as a RPG game, is horribly designed. It takes the learning curve and bends it into a brick wall, and throws the notion of reward based on challenge out the window.
One thing Factions has going for it is a better storyline...but then anything's better than the 'Let's abandon our people and screw up all time and space!' storyline from Prophecies.

Someone please tell me that once I get out of this city maze the game improves. The Kurzick/Luxon stuff looks interesting from a distance. But then, so did Cantha.