What profession do you play?
Do you plan to start any new professions because Factions will give you access to Ritualist and Assassin and Nightfall will give you Dervish and Paragon.
Although the Dervish should be getting an update Ritualist and ASsassin are two very propular professions for current PvE play while the others less so.
As for skills this could come down to your existing profession(s), my suggestion would be to look through the pvx wiki (
www.gwpvx.com) and there you will be able to see a list of the strongest and more popular builds used in the current game.
Then you can search for those skills on the wiki (wiki.guildwars.com) to see what campaign they are from. If majority is from Factions, get that, or if is Nightfall, etc.
Both Eye of the North and Nightfall will give you the option for Heroes, and Eye of the North also has the benefit of PvE Skills. Although both NF and Fac. also have some PvE skills available. Again look at the skills and what professions you're going to play.
After that you can look into end-game content. Factions has The Deep and Urgoz (both 12 man areas), Nightfall has Domain of Anguish (8 man with popular farming runs), Eye of the North has Dungeons of varying difficulty, some farmed, some not.
All areas including Prophecies that you own give you access to Underworld and Fissue of Woe.
One other thing to add is that if you're intention to return was to gain rewards prior to the launch of Guild Wars 2, then you will need Eye of the North in order to have a Hall of Monuments in which to store your achievements and thus gain their rewards in GW2.
Once you have a better understanding of what each campaign will offer you, you can decide which to buy based on their price. As has been mentioned, to get the most out of the game you are better off buying all the campaigns and EotN. However if you can't justify that cost then hopefully you can pick one and maybe purchase the others at a later date.
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