As a character from another campaign you will arrive in Prophecies or Factions at a later point than the start, I hope you know this. You will "miss" a portion of those campaigns, but it's not a big loss, in practical terms, because, like in Nightfall, they are meant as beginner tutorials. You can work your way backwards and do missions and such but you won't get XP for them. It can be useful to unlock the outposts for Zaishen missions, or for easy access during festivals, access to the weekly Nicholas location and farming the items for him, vanquishes, cartography etc.
Now, regarding your approach: ask yourself what you want from this game. If you're not interested in the story/lore and just want to unlock everything ASAP and grind for HoM, do what kajusbonus suggested. Strictly speaking, entering either Proph or Factions with a character and hero team formed in Nightfall will automatically be extremely overpowered and a major advantage.
If, however, you want to enjoy the experience of the first run through the game, I strongly suggest making a character in each campaign and doing it from start to finish at least once without using stuff from the other campaigns (heroes, skills, armor etc.) That first experience is something you will never get back once you've become jaded. I for one miss that magical feeling very much -- playing Prophecies for the first time was absolutely amazing -- but there's nothing I can do about it anymore.
For the time being, however, I think you're getting ahead of yourself. The first thing to do would be to finish Nightfall. The fact you're looking at Proph/Factions makes me think you like the dervish but perhaps not like Nightfall very much? You can also try EotN, but it might be a bit tough to swallow at your current level of game experience.
