You can play through both games with characters that started in either place with a few minor restrictions.
~ If you start in Prophecies you have to ascend your character to travel to Can.
~ If you start in Factions you can get a quest in the very first actual city you hit on the mainland that will lead you to the docks where you'll speak with Mehnlo who will let you travel to Tyr.
~ Unless you're character is going to be a Rt/A or A/Rt it's in your best interest to play through a lot of the Prophecies content for the sake of gaining skills, as apart from the starting island area in Factions there are no quests for skills. Many quests 'do' have a good xp award, some have skill points, and usually there's a small gold award as well. Sadly though, the 150 gold you get for a quest will only take a small chunk out of the 1plat per skill you'll be paying after obtaining the first few.
~ As far as what specific order you play the two in, again, since skills are rather expensive in Factions you'll have to do a lot of farming just to afford them, so it's in your best interrest to play through Prophecies first unless your main is either A or Rt. And yes, you can also switch your secondary in Factions after only a few missions at one of the outposts for a 500 gold fee.
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