Well, I would have Sylvonia use Mewtwo as a last ditch effort before Mike and Lily take on the Team Fusion leader, since Mega Mewtwo X has the highest attack stat out of all the 721+ Pokemon.
True. Alright we'll do that. Though by the time that Happens Samuel would have reviled himself as leader and have Sylock (Fire/water legendary created from the blood of the two main legendry's) and Kyiresom (Orginal dragon of Unova with x3 types)
I think that would depend on Nieve, Hanzo and Nic. Besides what if there is a second option and instead Mike and Sabrina give up there Lucario so they can stay toguther.
Well, they have to say goodbye to them, which means they won't be obtain or see each other ever again, they will become wild Pokemon once more until a Trainer catch them again, but since Sabrina has a female Lucario, which are rare to find since males are the most predominant.
And I said before, Mike and Lily are better together since they have something in common, while Sabrina Phoenix is sort of the black sheep out of the three.
I think you misunderstand. Warrior and Nic would still be Mike and Sabrina pokemon but they would be at ether of the professor labs to spend their life toguther.