In factions you get to lvl 20 like...within a day In Prophecies it takes a good while and ur deep into the game before your lvl 20.. If i was you play Prophecies first because it is the first game & its funner to be a noob in it
You can always power lvl yourself to lvl 20 by doing factions quests once you get to Lions arch ( a city which you arrive in about....... quater of the way into the storyline.) u should be like lvl 14 when u get there and lvling urself to 20 via factions is very useful to tackle the harder missions with the undead
Imo Factions is very boring to start off in. It has a wonderful storyline but the game feels a bit....rushed. I think its alot easier to start with Prophecies and then go into the easy factions if u go from Factions to Prophecies the change might be a bit odd for u to handle and might decide to stop playing
but to summarize
Factions is alot shorter than Prophecies
in Prophecies u lvl up slow when factions you lvl up mega fast talking about a quest that gives 3k exp reward when a Prophecies quest which is twice as long gives 500 exp
&
like 80% of the ppl who play Prophecies tend to be kinda newbie

in Factions i find that most ppl stick with the henchmen when Prophecies your pretty much forced to work with people unless u have a understanding of the game.
Hope i helped!