Fair, if he hits for just league average, he's a 3 WAR player. I think Waters can be a 5-tool player if it all clicks.
I tend to Waters because I think he has more offense upside. However, both are fine prospects and not that far away.
To me, the smart thing to do would have been to trade Inciarte, play Acuna in CF and sign Brantley and McCutchen. But that ship passed.
You could have used Inciarte as part of a bigger trade, say something LIKE Incarte, Newk and a minor leaguer for Kluber.
or
Just trade Inciarte for prospects say to Cleveland for Nolan Jones and Ethan Hankins.
If you went Bradley, Acuna, McCutchen (or Acuna, Pollock, McCutchen or Brantley, Pollock, Acuna) then you have both Pache and Waters left to fill a void when one or the other of the primary three goes down OR leaves via FA - assuming Brantley on a 2 year deal. Plus, you get whatever value Inciarte brings back. AND your OF defense isn't any worse most likely overall since Markakis isn't standing out there everyday. But even IF the defense does take a short hit, the offense would far outweigh the difference.
Instead, we've got a CF with a defense first pedigree under reasonable contract in a position of near term versatility and unable to play a position of need because of his lack of a bat.
It's not like Inciarte can bat LO or steal 100 bases. He's a pretty limited player who's best asset is well above average defense at a reasonable cost. A team constructed in a different way would hide Inciarte's bat and take the defense. The Braves, due to talent and payroll limitations, really don't have that luxury. But here we are.