Joe Root, in his first Ashes series as captain, oversaw a comprehensive 4-0 defeat by Australia in a one-sided set of Test matches.
The Yorkshireman was forced to tour without his best player, with all-rounder Stokes suspended for all five Test matches due to an ongoing police investigation into his September arrest outside a nightclub in Bristol.
The 26-year-old eventually joined the squad in New Zealand earlier this month after pleading not guilty at Bristol Magistrates Court last week to a charge of affray.
And Waugh reckons Stokes will have to pull more than his weight for a prolonged period of time after missing so much cricket.
“It’s been chaotic and a bit of a circus,” said Waugh ahead of the Laureus 2018 World Sports Awards, which both celebrate sporting excellence and harness the power to sport to promote change.
“He certainly owes his team some good performances over the next couple of years because he really put them in a bit of a hole with the Australian tour which was unsettling for the whole team.
“And for Trevor Bayliss and Joe Root to continually front the media and answer those questions, that’s wearing on those players and it was tough on Joe.
“I’m sure he has learned his lesson from what has happened and he left England in an awkward position. It put them off kilter for the whole trip and they didn’t really recover.”
But Waugh, who captained Australia 57 times and won two Ashes series as skipper, was quick to praise the way he dealt with the Stokes issue Down Under.
“Joe couldn’t have handled it any other way. It was awkward as the police hadn’t made a decision, the jury was still out and you had all of the video footage out around the world,” Waugh added.
“These days, if you do something like that everyone has access to it so it was always going to be talking point.
“And then the Bairstow thing came up and a couple of other things, which on any other tour would have been non-events but then they become magnified and all of a sudden you’re dealing with problems every day which you don’t need to. It just became a bit of snowball effect for the team.”
***The Laureus World Sports Awards highlight sporting excellence, but more than ever the Awards celebrate and recognise those who use sport to change lives for the better. For more information, head to www.laureus.com/awards***