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 EFL Cup is a "total rip-off" for fans because Premier League managers field weakened teams, says former England winger Chris Waddle.