While there is no doubt that Duckett, Billings and Malan have a bright future ahead of them, this England team, as currently constructed, is playing some very good limited overs cricket, something that hasn't happened in a long time.
To have played Billings either Bairstow or Buttler would need to be dropped. To have included Duckett, either Hales or Roy would need to sit, and to fit Malan into the side either Morgan or Root would have been forced to miss out.
No easy decisions there. My team for the ODIs would be:
In Morgan's defence, his average (36.31) and strike-rate (87.63) over the last 12 month are almost identical to his career average (36.67) and strike-rate (87.16). His numbers batting 4th have also been much more impressive over the last year, averaging 41.23. As a collective unit, No 4s have averaged 39.82 over this same period. So he has been above average when batting at No 4.
Morgan should also be given credit for the way this current England team is playing. There has been a complete change in the mindset of the squad. They are far more aggressive and fearless with both bat and bowl.
For this reason alone, I wouldn't advocate replacing him in the side.