My guess would be Ninian. Not only does Eliwood's relationship with her impact the ending of the game, but the joint character ending between the two describes Roy's endeavors in a more unique way then his pairing with Lyn or Fiora. Check it out:

Eliwood and Lyn
The marquess of Pherae and the princess of Caelin were wed after the conflict. All of Lycia was in an uproar, but none could sunder their bond of love. They have a son named Roy, who will become a great hero.

Eliwood and Fiora
Eliwood and Fiora were wed after the conflict. A group of Lycian nobles protested that she was a mercenary, but none could sunder their bond of love. They have a son named Roy who will become a great hero.

as opposed to:

Eliwood and Ninian
Eliwood and Ninian were wed after the conflict. Ninian gave up her old life and her people to enjoy a brief life with Eliwood. They have a son named Roy, who will one day take up arms to defend his nation.

To me, it will always be Ninian as Roy's mother.