The scheme doesn't make it so that you can't have a good deep threat, it just makes it harder to draft a late round receiver whose only positive attribute is speed and turn him into a stud. I think we're going to see more draft busts for the human players and it's going to be much harder to turn late round picks into starters much less all pros.
One other positive change I think will arise from this new system will be an increase in the number of players who will only be useful to your team for 1-2 seasons. Now that receiver you drafted in the seventh round may not turn out be good enough to justify letting him finish his rookie deal if they regress early due to not putting up enough stats. If we're really lucky we'll get late round players who aren't even good enough to make your active roster but that other teams might have a use for in FA.
Hopefully archetypes in the draft are distributed in such a manner that you can't always pick players best suited to your scheme because their ability simply doesn't justify spending your current pick on them. NFL teams encounter this dilemma constantly.