Ahh, Guild Wars. About 500 hours on it myself, mainly PvE.
The first game I got was factions, and thoroughly enjoyed every aspect of it, and still do. Though I have been told time and time again how great prophecies is, but could never get into it. Mainly because the gameplay starts slower, giving more room for practice, and focuses in on more basic skills.
I highly recommend Prophecies as you first game.
Nightfall is sucks up until about halfway through, and then spices up.
NF is much more harsh to "newbs," as it doesn't give much of a tutorial, in fact, you have to bugger off until yo get to level 5 at the start, with no directions whatsoever.
So yeah, for beginners, Proph > Factions > NF > EOTN.