I have played Eclipse (1x), and Twilight Imperium (10x)
I think I prefer TI.
Core differences:
Eclipse plays much faster (no more than 1/2 the time of TI3 game)
You get to design your own ships in Eclipse
There are more ship types in TI
TI has a simpler resource model
Combat is less meaningful in TI (~1/3 of your VP in eclipse come from combat)
I just found that as the leader, it was much harder to maintain control in eclipse relative to to TI3 - as you can't take away someone elses VPs, and if the other players want to gang up on you, they potentially harm themselves by doing so.
Thus, the end of the game politics were very frustrating in Eclipse.
I don't mind the extra time, but you have to realize that Eclipse is a game that you can potentially bring out on a normal game day, play it, and then play something else.
TI3 - that is your whole day and then some.