Alder - I can see him still in the game, just not as the role of Champion. From what I thought he didn't really feel like dealing the the role that a Champion has to deal with i.e. manning the helm at the League. So I could see him pass on the title to his apprentice Marshal or Cheren who already beat all of them right after the character did. Alder strikes me as a traveling that goes about the region and helps where he can and takes in the pokemon world, which is what he seemed to be doing at times in BW. I can see the character being able to face him post main story, and him assisting the character in a double battle like Lance and Steven have done in the past.
N - As already mentioned there seems to be a lot left open with his story that has yet to be resolved or explained. His return more then just about any prior character seems essential to me. N needs to resolve the conflict with him and Ghetsis and thwart whatever Ghetsis has in mind. I can see N playing the role of the silent protagonist that helps when needed again maybe Plasma or whomever else is present.
Ghetsis - Him and N return seem interlinked imo. As with N his story seems unresolved as he got broke out of prison, and then what? Did he start a new organization, did he go into hiding, did he go to another region? I would like them to fill in the blank for me. And then ultimately have him properly deal with what he put N through and the crimes he committed.
Cheren - I think he would be good as a gym leader, elite four member, or Champ. He has proved to be strong in the previous game, so maybe he may some notable improvements with the time skip as well.
Bianca - I can see her either being Juniper assistance(obviously pending Juniper is there) or playing some sort of role in Pokemon Musicals. Other then that I don't see what role she would really play.
Juniper(s) - I can see both of the Junipers still in Unova, what role they may play though may be different. Hopefully you can get another regions starter for Aurea though.
Looker - I would rather see another international police member this time around. I mean Looker can't be the only officer in the police organization. More then likely he will stay, but I'd like to see a new officer.
Cynthia - She may be at the Villa again, but if there is a Champs League I'd rather see that instead.