That's a tough call.
Factions offers faster levelling, quicker gold gain, more affordable armor options, the Ritualist and Assassin professions, faster paced PvE, a lot of PvP gamestyles, plus better music.
Nightfall offers Heroes, a richer PvE storyline, better cinematics, inscribable items and armor, and the Dervish and Paragon professions.
Having played through all three, I find myself enjoying Factions the most these days. However, that is with heroes... I don't think I'd feel the same way if I were dependent upon pick up groups or henchmen. In Factions, a lot of the higher level PvE areas can be fairly empty; but if one is in a helpful guild, that isn't such a big issue. Before heroes, I remember having to wait several days or more to find a group for certain missions.
Nightfall is great; yet having completed it with one character, it just doesn't draw me into playing through the missions and quest areas much with my other characters. The only reason I do is to unlock heroes. And one has to play through a considerable part of Nightfall to unlock the cooler heroes.
If storyline consistency is an issue, play through Factions first and then Nightfall. If it's not, I'd recommend playing Nightfall first, and then after the game is complete and all heroes are unlocked, like General Morgahn and Razah the Ritualist, then play Factions. The PvE will be more fun with all the heroes unlocked, and you can move into the more interesting PvP from there.
Edit: It's kind of interesting how the Ritualist hero Razah is unlocked after one completes the Nightfall campaign. It makes one wonder, "well what do I use him for, since the game is over now?" I think it's to encourage those who haven't played Factions to pick it up, since all of Razah's good skills are unlocked in Factions. Plus one doesn't get to unlock Zenmai the Assassin without Factions. Fwiw, it's pretty cool to play through Factions with a Rit and Assassin hero along. And the storyline consistency issue isn't really that big of a deal with regards to Nightfall and Factions, ie. they could plausibly be played out of order and things still make sense. It's more of an issue with Nightfall and Prophecies, regarding the five Gods and Abaddon.