Ego has actually had five or six different origins, depending on how you count them.
1. Ego was a sentient planet which existed at the center of the Black Galaxy, described as being a fluid bio-verse.
2. Ego was originally Egros, a member of a sentient humanoid race. When it was discovered that their sun would be going nova at a very precise time in the future, Egros led the efforts to save everybody. Sadly, the time when they calculated their sun would go nova was a bit (less then one minute) off and Egros was caught by the radiation from the nova while outside the shielded chamber which had not been sealed yet because he was still outside. As a result, the nova's radiation fused the mind of Egros and the lifeforce of the rest of his race with the matter of the entire planet to create Ego the Living Planet.
3. Ego was a unique but naturally occurring lifeform. The whole Egros origin was a fiction contained within a small false brain which Ego used to deceive enemies into being more sympathetic to him. Ego's real brain was much larger (Moon-sized) and located at the center of his mass.
4. Ego was possibly a component of a massive creature known as Super-Ego that was opposed by the Celestials. Also, the Black Galaxy was either created by the Celestials or taken over by them so that a new Celestial could be born.
5. Ego and his brother Alter Ego were both created long ago by the Stranger as part of one of his experiments. Ego was unaware of his brother's existence until recently. Alter Ego, maddened by being held captive by the Collector since his creation, attacked Ego who was then forced to defend himself, causing his brother to lose much of his mass. Thor's intervention prevented Ego from destroying his brother and the two of them made peace with Alter Ego becoming Ego's moon.
6. Ego was once Egros until a Stranger caused his world's sun to go nova and consume its twin planets, possibly in order to create something like Ego. Egros' race died but Egros survived and became one with every particle of matter that made up his planet.
Although I really like what Al Ewing did to make Nextwave "canon" in Reality-616 and how he explained the origin/history of the multiverses, I must agree that this revision of Ego's origin is not as good. The problem is, I'm not sure why. Maybe it just feels a bit off to me. Or maybe the fact that it was assembled from elements of different stories that don't naturally fit together is something that shines through the cracks.
I always sort of liked the idea that he was a unique thing that just was, but really any of them works.