Well as things are going, the spotlight is on Yuuno and he's the one confronting Fate, and hence basing on his character he most likely will try to save Fate as well; though mostly because Nanoha wanted to in the past. So instead of Nanoha being Fate's first friend, Yuuno will become the one instead. So it's not hard to imagine that sooner or later Fate will develop romantic feelings for him.
Whereas for Nanoha, well, would any author who writes about Fate ever leave Nanoha out of the party?
Regardless of what they story may be in the future, Yuuno is definitely the main character for this story. There are two possible main branches I can see here, both assuming Precia knows about the time travel and interfere: One, everything was reset at the end (on a happy note) and Yuuno returns to the moment before the Jewel Seed activated, and succeeded this time at stopping it (or it stopped by itself as how original history should have been). This is considering the factor of Nanoha 'remembering' her past a Magical Girl.
The second one would be that they concluded the battle without going back and Yuuno remains the MC since he'll be a lot more confident about himself and active than the original MGLN, and the story's title will forever be changed to Magical Boy Lyrical (o_@) Yuuno. Lol.
The fact that it's so
possible is what I admire about this author; he created exactly the turning point that will decide whether Nanoha or Yuuno will become the hero of the series.
EDIT: No idea whether it has a subtitle. Calling private Raiser!