Liverpool made 11 changes and Tottenham 10 on Tuesday and the 10 top-flight teams made 71 changes, with a number of young or fringe players involved.
"I feel for the fans," said 55-year-old Waddle. "They should know who is going to play in the competition."
Former Tottenham manager David Pleat also said he was "very disappointed".
Pleat, who reached the semi-finals of the competition in 1987 as manager of Tottenham, said teams are treating the competition as a "secondary affair".
"It is almost as if the Premier League clubs have got together and said we are not going to give the competition our full attention," he said.
Ex-Spurs and Newcastle player Waddle said clubs should announce their squad for the cup's fixtures in advance at the start of the week.
"It would mean that if you're travelling a long way you'd know that it will be a weaker side and you may not buy a ticket," he told BBC Radio 5 live.
"For me, it is a total rip-off."
Tottenham manager Mauricio Pochettino, whose side are fifth in the Premier League and second in their Champions League group, defended his decision to use some of the younger members of his squad in Tuesday's 2-1 defeat at Anfield.
"The young players are very important for our future, to be a better squad," he said.
"I think it was a fantastic opportunity to show their quality and a great experience to capitalise on, to take positive things for the future."

The Heritage Lottery Fund said the project lacked backing from Conwy council and was deemed "high risk".
The council has applied to have the Grade II-listed structure demolished.
However, a protracted legal dispute over the ownership of the pier is still rumbling on between businessman Steve Hunt and the council.
The bid for lottery cash from the HLF was made by the Colwyn Victoria Pier Trust, who described the request as a "last chance" for the pier.
Announcing that the funding bid was unsuccessful, HLF's chief executive Carole Souter said: "HLF takes its role of investing National Lottery players' money extremely seriously and we only support projects that we are confident can deliver long-term benefits.
"Unfortunately, we have not had a clear enough indication of strong support from Conwy County Borough Council.
"In light of this as well as the absence of other confirmed financial support and the potential for increased costs, the application was deemed high risk."
The campaigners trying to save the pier said on Wednesday they were "bitterly disappointed" by the decision.
Conwy's council leader Dilwyn Roberts said he realised the pier trust would be disappointed, stressing that the authority would continue to talk to the trust and Colwyn town council and "would welcome talking to them further about proposals for legacy".
However, restoration is not on the council's agenda following the HLF announcement.
"As the application was unsuccessful, the council's application to demolish the pier will continue through the planning process," said the council leader.

Anaya Ellick from Chesapeake, Virginia, does not use prosthetics. To write, she stands to get the proper angle, holding a pencil between her arms.
Her principal, Tracy Cox from Greenbrier Christian Academy, describes her as an "inspiration".
"She does not let anything get in the way of doing what she has set out to do," says Ms Cox.
"She is a hard worker and has some of the best handwriting in her class."
The girl reportedly beat 50 other competitors to get the special-needs category prize at the National Handwriting Contest.
This category rewards students with an intellectual, physical, or developmental disability.
Competition director Kathleen Wright told ABC News that her "writing sample was comparable to someone who had hands".
This is what her winning entry looked like:
Sponsors of the contest Zaner-Bloser said they planned to award each student $1,000 (Â£690).
They tweeted a picture of the student, happily holding her trophy.
Having no hands was also not an obstacle to 30-year-old pilot Jessica Cox.
In 2013, we reported on her inspirational example.  Also born without hands, she has been able to drive a car, fly a plane and play piano - all with her feet.
The EFL Cup is a "total rip-off" for fans because Premier League managers field weakened teams, says former England winger Chris Waddle.
[NEXT_CONCEPT]
Colwyn Bay's Victoria pier has failed to win a £9.6m bid for lottery heritage restoration cash and now faces demolition.
[NEXT_CONCEPT]
A seven-year-old student born without hands has won a US national handwriting contest.