Duckett batted at No. 3 in Bangladesh and scored two half-centuries in three innings. But although Bayliss said he had "shot up the pecking order" the selectors eventually decided to stick with the squad that has served England well for the majority of the last 18 months. England have won nine of their 12 most recent ODIs.
There was, according to Bayliss, never any doubt that Morgan would return as captain. Though the England management were disappointed that he and Hales elected not to go to Bangladesh due to their security fears, the ECB had specified months ago that those who skipped the tour would not be punished for doing so.
Root, who was rested from the limited-overs section of the Bangladesh tour, is also back and set to reclaim his spot at No. 3, despite expecting the birth of his first child a few days before England return to India in January. The combination of those factors meant no room for Duckett.
"There was a lot of discussion around Duckett," Bayliss said. "It was the toughest decision and the one we spoke about the most. He did well in Bangladesh and if we had left someone else out they would have been desperately unlucky as well. We thought that Duckett has done himself no harm. He has shot up the pecking order and he is right there or thereabouts.
"At this stage he is more suited to white-ball cricket and he showed he had what it takes in Bangladesh. There were a couple of innings there that were class. He has done well for himself but we thought we would show a bit of solidarity with the team we have had and done so well in last 12-18 months."
James Vince, who scored 53 runs in three ODIs in Bangladesh, has also been dropped, as was Steven Finn, who was a member of the squad but did not play in Bangladesh. The selectors resisted the temptation to rest players, reasoning that the gap between tours - the players will have more than two weeks at home between the end of the India Test series and their departure for the limited-overs games - was adequate.
Bayliss did hint, though, that Moeen Ali and Ben Stokes "who have played a fair bit" may be rotated in order to allow "someone like Liam Dawson ... another opportunity".
With Morgan, Hales and Root all but certain to return, Duckett was competing for inclusion in the squad with Jonny Bairstow and Sam Billings. In the end, though, the selectors decided Bairstow and Billings were better players of spin and wanted to offer more opportunities to those regular members of the squad.
"Billings and Bairstow at this stage are probably the two spare batters," Bayliss said. "We think both are two of our better players of spin. Billings did well with the opportunity he had in Bangladesh and Bairstow has been batting well. Probably over the last couple of years, due to strength of the team we have had, he has not had the opportunities he would have liked. He is a good player, we all know that, and we want to keep him involved.
"Hales has made four hundreds and ODI cricket suits him to a tee. He has that bit of extra time to get himself in and when he gets himself in we know the damage he can do from a batting point of view. He has been an integral part of the last couple of seasons in white-ball cricket. He has not given up hope of continuing in Test cricket either, but at the moment he is not there and extra focus is on one-day cricket. He has certainly been one of our better players in white ball cricket.
"I have not had the chance to speak to Duckett yet but my message to him will be 'Mate, well done, you have had a fantastic start and see this as the beginnings of a career. Keep going out and scoring runs because you are right there or thereabouts.' This decision was more to do with the experience of the guys we have in the team who have been together for the last 18 months and done well.
"The Champions Trophy is one of the big tournaments in the world and we are playing at home. We want to be in as good a form as we possibly can, so we don't want to be chopping and changing the team leading into that tournament."
Bayliss confirmed that Morgan had been involved in the selection of the squad and dismissed the suggestion that his authority as captain had been diminished by his decision to miss the Bangladesh trip.
"Morgan not returning as captain was not even discussed," Bayliss said. "It was said earlier that there would not be any recriminations against them and they are straight back in. We have done pretty well over last 18 months and the team we have got has been reasonably stable and successful and there is no reason to change.
"I have not sensed that his authority has been eroded at all. There has been no comment about it. He gets on well with all of the guys in the team. He is very highly respected among everyone for the job he has done over the last two years. He captains the team very well. He is a very positive captain and that means a lot to the players in the team."
Other notable inclusions were Dawson being named in both squads - he was last week called up to join the Test party - and Tymal Mills in the T20 squad. And, while Bayliss acknowledged that Moeen and Adil Rashid "are the two best spinners" England have, he did name check Hampshire's 19-year-old legspinner, Mason Crane, as a bowler with "reasonable control" and a player who had impressed him.