Differences between this and the original?

Depends on what you're comparing.

First Eon box: 15 aliens, attacks and negotiates, basic artifacts.

Eon + 9 expansions: 75 aliens, flares, moons, lucre, more attacks and artifacts, reverse cone.

FFG base box: 50 aliens, attacks and negotiates and a morph, basic artifacts, flares, reinforcements, tech.

FFG + 2 expansions: 90 aliens, reward deck (more attacks and negotiates and kickers, more artifacts, rifts), hazards.

I'm probably forgetting minor other stuff.