I am new to GW which you will probably be able to tell by the questions I am about to ask.

First let me give you a little background, me and my friend have decided to play through the entire story of guildwars. Right now we are up to mission 13 in prophecies. Things are beginning to get a little tough for us. So I was wondering if I were to go to factions and get a few new skills there if it would affect our gameplay in prophecies. I.e. would I still be able to go through the missions with him? Or would I be stuck in factions? I am lv18 and I am an Elementalist / Mesmer who currently spams flare, fireball, firestorm for AOE, and of course epidemic for when my friend uses disease or enfeeble. My friend plays a Necromancer / Monk, specializing in making minions to do his bidding. If you need more information I'll be happy to post. But all in all I am asking if there is a place where i can accumulate some more powerful skills without getting ahead of where we are in prophecies (Keep in mind this char will not be doing the storyline in factions or Nightfall, if he gets ahead in that respect, that is fine).
For those who hate to read long paragraphs, the short version: What skills do you recommend I use for an E/Me who has at the moment only prophecy skills available up to mission 13 (level 18). I Play with a N/Mo, so any skills that work well with that class would benefit me as well. And will going to Nightfall or Factions screw up our storyline in prophecies?