Alastair Cook’s men secured a draw in the final Test in Nagpur to wrap up a 2-1 victory on the subcontinent after suffering a heavy defeat in the first Test in Ahmedabad.
“Here [in India] we have shown we can learn and adapt and overcome,” Flower told BBC Sport.
“We did not play that well against the spin in the United Arab Emirates, but we have also done superb things.”
He added: “I certainly would not describe this year as a year of decline, that would be careless in the extreme. I think we have had up and down results.
“We became number one in one-day international cricket, we drew an important Test series in Sri Lanka, we won a Test series against the West Indies and we lost to a very good South African side in England.
“I do not think there was any embarrassment in that.”
An ECB statement read: “Woakes and Buttler replace Anderson and Trott in the India ODI squad as the selectors look to manage workloads.”
Eoin Morgan will captain the T20 side for the internationals against India on 20 and 22 December, with Joe Root also included in the squad.
Twenty20 squad: Jonny Bairstow, Tim Bresnan, Danny Briggs, Jos Buttler, Jade Dernbach, Alex Hales, James Harris, Michael Lumb, Stuart Meaker, Eoin Morgan (capt), Samit Patel, Joe Root, James Tredwell, Luke Wright.
ODI squad: Alastair Cook (capt), Jonny Bairstow, Ian Bell, Tim Bresnan, Danny Briggs, Jos Buttler, Jade Dernbach, Steven Finn, Craig Kieswetter, Stuart Meaker, Eoin Morgan, Samit Patel, Kevin Pietersen, James Tredwell, Chris Woakes.