If and when Hotaru awakens her senshi powers, a) she'll be put on a power limiter like Nanoha/Fate/Hayate, b) Uranus and Neptune will still try to kill herPutting them as direct enemies of Nanoha and her senshi since they can't comprehend that Hotaru's powers can be limited so she doesn't destroy the world. Cue befriending by Nanoha.
The Black Moon Clan is effectively neutralizedConsider this. Nanoha, by all indication, has no intention of reviving the Moon Kingdom, and barring something forcing her to (prime candidates: Luna or the Ginzuishou itself), she probably won't ever claim her birthright as the Moon Princess. Hence, she won't become queen of Crystal Tokyo, hence she won't try to cleanse the Earth, hence the Black Moon Clan can't reject her, hence she can't exile them, hence resentment can't build up and cause an attack.
Luna will lose it.Considering how Nanoha refuses to accept her birthright, which runs contrary to everything Luna believes, Luna may attempt to force Nanoha to accept it, whether she wants to or not. This may also be because her position of power is null right now, and she wants it back at all costs.
They'll go back and forth between Nanoha villains and Sailor Moon villains.On the Nanoha side, there's still Jail and co, Ixpella and the Mariage (which will probably play out similar to canon, seeing how Ixpella doesn't WANT to be a villain), and the Huckbeins. On the Sailor Moon side, since Mistress 9 and Germatoid are already gone, that still leaves the Dead Moon Circus, Shadow Galactica, and possibly the Black Moon Clan. I think we've got more teamups on the way.
Raising Heart will change form in the battle against Metallia.She'll incorporate the Ginzuishou into her design so Nanoha can use both it and her to defeat Metallia.
Beryl will Heel-Face Turn.Nanoha will befriend her the hard way and Beryl will finally see reason and be free to pursue Mamoru, therefore turning on Metallia and helping Nanoha and co. Unless the omake that hinted at Mamoru/Rei turns out true.
The paradoxical Picohaverse was a dystopia anyway.In fact. That's the world that would have happened had Nanoha been forced to revive the Moon Kingdom. Stuck with a kingdom she doesn't want, stuck with a husband she doesn't want (since the Moon Kingdom needs an heir and won't take Nanoha being a lesbian for an answer), Nanoha would have neglected it, run it into the ground, or surrendered it to the TSAB as soon as Luna wasn't looking. Not that Picoha knew that, she was sheltered.
The Outer Senshi's reaction to Nanoha absolving them of their dutiesWell, first off, it would take them a long time for them to even hear about it, cause Pluto is at the Time Gate, Uranus and Neptune are doing their own thing, and Saturn has not awoken. However, once they DID find out, it's quite possible that Uranus and Neptune will either challenge Nanoha herself, or swear fealty to her anyway and join the TSAB, becoming the Wolkenritter to her Hayate. Pluto would probably still guard the Time Gate under the justification that she had sworn to Queen Serenity and therefore still had a duty. As for Hotaru? She might never awaken as a Senshi, particularly if she does choose to join the TSAB and the put a power limiter on her before she can awaken.
Given an opportunity, Luna might Face-Heel Turn.It might be just me, but it seems like Luna is desperate for the Moon Kingdom to be revived because she wants her position of power as the Queen's chief adviser back. If she was desperate enough (and years of trying and failing to get Nanoha to revive the Moon Kingdom would do that) she could ally herself with someone powerful and villainous, cause better power under a villain than no power under Nanoha. She could even undergo a transformation similar to Vivio or Black Lady to gain power for herself. (Cause honestly? I could see WDOTM!Luna try to usurp the throne.)
Hotaru will learn ninjitsu.She did get adopted by the Takamachis after all
Pluto could bypass the stopping time=death tabooHow? Simple. Equipping the Time Staff with a cartridge system.