If you're only getting one you should get Prophecies if you want an RPG or Factions if you want a more PvP oriented game. Personally, I think the storyline in Factions is mildly put bad, especially when compared to Prophecies, which has a story it actually takes longer then a day to play through. In Factions you don't need to do any PvP, but to me it seems they intended it much more as a competitive game then a storydriven game.
But then again, both are great supplements to eachother, so if you like one chances are you want the other
-edit due to new post-
There are lots who play Prophecies despite having Factions, I just restarted Prophecies today, and both pre- and post-searing are teeming with people.
(note: pre-searing is an area you can't get to later in the game, it's reserved for new players)