A lot of people don't seem to realize that Ultimecia was in possession of Edea, Rinoa, and Adel at various points in the game. This is fairly clearly explained during the game. She wasn't a villain that just popped up at the end of the game. She was present from fairly close to the beginning, right through to the end. Her character weaves throughout history, and all of the events of the main story revolve around Ultimecia's quest to unify the powers of the Sorceresses to awaken the full power of an ancient God (which is why, Rinoa is referred to as "Daughter of Hyne" in the game).

Essentially the story goes as follows:

Distant Past
1. In the past, the God Hyne was defeated and his powers were split up among the sorceresses.
2. Over time, sorceresses passed on their powers to successors, and they became more powerful as certain sorceresses inherited the powers of 2 sorceresses - this is seen towards the end of the game when viewing the history of the sorceresses, you battle multiple weak ones, then gradually fewre but stronger ones.

Laguna's Time
3. By the time of Laguna's youth, when Raine and Julia were still alive, there were only two Sorceresses, Edea and Adel.
4. Adel mysteriously disappears from history; this was because Laguna locked her up in cryo-storage and shot her into space. Adel's powers do not pass on.
5. Dr. Odine begins creating the Ellone Emulator.
* In the future, Ultimecia is attempting to gain unlimited power, she can go back in time as far as this period using Odine's Ellone Emulator. She can only go as far back as the Emulator's existence.
6. Edea bumps into Ultimecia at the orphanage, and when she absorbs her, she realizes that the power is hers, and that Ultimecia is a wrathful figure from the future with intentions.
* It is here that SEED is born in order to battle the sorceress.

Squall's Time
7. Ultimecia transfers her consciousness back in time and possesses Edea, Ultimecia is now effectively using Sorceress Edea's body. Her goal is to find Sorceress Adel, and to absorb her to unify the ancient powers of Hyne (kind of like how Highlander unified the knowledge of the Immortals by killing the others off).
8. When Ultimecia can't find Adel, she discovers she has to go further back in time, and seeks out the real Ellone who lived in the time of Adel.
9. Adel is discovered, Ultimecia uses Seifer and Rinoa to retrieve her body from space.
10. When Adel's body is found, Ultimecia possesses and awakens her, and uses time compression to bring her body to the future. Time compression allows the transportation of more than just consciousness, but matter as well.

Future:
11. Ultimecia somehow becomes corrupt, SEED of the future attempt to stop her, but are destroyed.
12. She sends her consciousness back in time to find the rest (the stronger part) of the sorceress powers (in Adel's body).
13. She can now merge with body of Adel and resurrect the full powers of Hyne.
14. Squall and company defeat her.
15. Her body is thrown back in time, and she wanders into sorceress Edea who absorbs her power.

I see lots of hate for her. I luvd her as a villain of the game!

Necron wasn't actually a villain, he was just a boss fight. He doesn't count in this discussion!

Actually he was the villain. He's the one that wanted the entire world to go back to nothing, because he himself was nothing. Kuja just threw a hissy fit against Garland and Zidane when he went batshit insane in Terra

Kuja and Garland are still the ones who engineered everything: Necron only took notice of the party when you took out Kuja.

"What up bitches, I heard the party you was having, now I will destroy you"

He wasn't relevant to the plot in any way; not actually a villain at all.

Yet the goals of both Kuja and Garland didn't even revolve around the crystal until Kuja went Berserk

The entire 4th CD was just an excuse for the introduction of Necron. Of course he wasn't relevant to the plot, but the fact is that he was the only one that trully had a unshattering motive to destroy everything. 

I don't agree with his introduction as I don't think it ever made any sense. The game would have been just fine if it had ended with Trance Kuja.