I have a great idea
each of the blacklist members have a legendary after you defeat them they give their legendary to you!
and the first two people have mew and mewtwo!
so then you can give them to the professor but the professor could fuse them and make a new pokemon combining the two pokemon and make mewthree using those so mewthree=mew + mewtwo ,isnt this better than mixing their DNA?
and after he does that the mewthree gets angry and wild and runs away to top of a mountain but you gain access to that mountain after you beat number 4 !
how is that?
oh wait I siad before that each member should have a legendary well since there are so many legendaries one member could have all the legendary cat and after you beat you get to choose one the other member could have the birds, and the other one could have lugia and ho-oh ,the other one groudon kyorge , and so on...
oh and the starters could the evoloution of evee so you can choose any evolved type! like flareon and jolteon and ...
and the professorr doesnt give you the first pokemon because he has given you one already so you buy one from a mysterious guy that comes around your hometown! or you could borrow one from a friend :D or you could save somebody's life and as a thank you gift he gives you a pokemon of your choice. or you could find an egg!