There are actually several points along story/quest lines that change for characters who beat nael in 1.0.
1.) The intro scene, when you go to register at the adventurer's guild the npc says something like "funny, your name is already here...".
2.) When you join the scions, Minfilia remembers who you are, but no one else does.
3.) In the CS where you're riding the airship with Cid to face Garuda, he explicitly remembers you as the one who challenged Nael with him in 1.0.
4.) After you beat Ultima, everyone else remembers you.
In case anyone wants to know how the "legacy" CS goes :
Merlwyb : He's still in there...
Raubahn : Cid! Has there been no word?
Cid : Nothing. Nothing at all.
Papalymo : Damnation!
Yda : He's going to make it. I know he is!
Y'shtola : Yda is right. We must have faith.
Kan-E-Senna : Cid, can they not be evacuated aboard the Enterprise?
That adventurer and the Scions are as the warriors of light reborn.
We cannot abandon them to their fate! Not again!
Cid : I wholeheartedly agree! But flying into the midst of that would only add to the fireworks!
Alphinaud : There must be something we can do!
Minfilia : Please mother Hydaelyn, please light his way through the darkness...
"Look into the light my child. If thou wouldst see thy companions returned safe to thee, reach out to them now."
Y'shtola : It's him. I feel his presence!"
Yda : Can it be...? Is it really him!?
Papalymo : I knew it! I knew it all along!
Kan-E-Senna : Who speaks...? The Crystal! She calls to us!
Merlwyb : I hear her! The voice of Hydaelyn Herself.
Raubahn : She speaks of...
Strike me down! No wonder he seemed so familiar! He's one of the Warriors of Light!
What are you smirking at Cid? You knew didn't you!?
Cid : Oh, You mean our adventurer friend? Did I forget to mention he was one of the Warriors of Light?
Saved Eorzea you know. Twice.
*Minfilia wipes away a tear*
Minfilia : The shroud is lifted. They remember you...
There!
*cutscene continues as normal*