I would tend to drift more towards Prophecies, but following is a list of pros and cons for both.
>Factions leveling time is much quicker
>Prophecies is much longer(25 missions vs 13 for Factions)
>In Factions you pay for all skills period; Prophecies lets you gain the majority of them through quests
>Prophecies is geared for PvE, Factions is much heavier towards the PvP aspect of the game. (which is why it is much shorter)
>Factions has closed doors so you're forced to play the game all the way through; whereas in Prophecies you can be ran almost anywhere. I highly suggest that you at least finish Prophecies once without being ran anywhere though, or you'll lose out on the experience.
Hope I helped