I just merged these two.
Here's how I would do the split - They need to establish who the GM's will be and where as early as possible. Then, ahead of the draft, instigate the idea that top tier talent can actually be bargained and competed for and won over by GMs. Add that extra element of storytelling that can be worked constantly during the year as the GM's hold secret meetings trying to "woo" stars to their brand with promises and offers.
Then for everyone else, you have a draft. During the draft, take a handful of NXT stars who might be ready and make them eligible. Joe, Aries, Bayley, Blake & Murphy for example. But I like the idea more of Shane & Steph meeting with say, Balor, and offering him this and that to sign with their show.
Actually, any star is eligible to be actively pursued (or sell themselves) by the GMs during a certain period prior to the draft and if they sign one place or another then that automatically removes them from the draft. I think that would be so entertaining and has the potential for longevity, if done right.
There's a hot internet rumor (that I made up, Meltzer style) that WWE will make Bobby Roode their first Smackdown champ. They won't but that would be awesome if they did.