Alright I'll order my responses in the same order of your questions.
-I think that Black will keep
Reshiram because in Pokemon Special, Dexholders have kept legendaries before. Also, I think
Zekrom will go to White after the big Black vs. N battle so that White will have something to fight with when battling Ghetsis.
-I think Gigi will stay with N because White already has a starter and if
Samurott goes with Hugh, then it will continue the starter cycle with male:fire, rival: water and female: grass after it was grass-fire-water last time. Know what I'm talking about, right? And N is a rival to some extent (I know he's not considered an official rival but still). Cheren and Bianca, the two rivals without Dexes like Wally, have unevolved starters so if N keeps Gigi then it will complete the web with the three non-Dexholder rivals owning each of the starters.
Also, I'm almost 100% certain that Nate and Rosa will just be Black and White in new clothes like Crystal. If Kusaka includes separate characters for Nate and Rosa then he will need even more starters, more Dexes and he already ran out of games to name the main characters after. It is so much easier to just slap on new clothes onto Black and White and make Hugh the rival Dexholder. With this method, the only dilemma left is that Hugh is the first main character not to be named after a game, which was bound to happen eventually anyway.
-I'm not too sure about this one but it's probable the Giovanni gave
Ursaring back to Silver and so Silver gave
Rhyperior back to Blue. That's the best option, since Blue has Rhyperior in the games and Silver only gave Ursaring to Giovanni so that he will have a caretaker while being sick. Giovanni already has enough powerful Pokemon.
-That was never mentioned but since Green never used any of the legendary birds in future appearances she probably released them. If not, then they're in storage.
-Like I said before,
Nate and Rosa will most likely (and hopefully) be Black and White in new clothes. For X & Y, they will most likely follow the pattern so the boy will get Froakie, the girl will get Fennekin and the rival will get Chespin. It's convenient too since (not trying to be sexist here) Fire-type starters don't always look like the kind that a girl will choose but
Torchic was cute enough for Sapphire (then again she's not really into "cute" Pokemon) and Fennekin looks cuter than the usual fire-type starters as well.
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