O'Neill is aggrieved in the same way regarding the Stoke players having a full week off, after their match with Fulham was rearranged because of the Cottagers European campaign.
In contrast, Villa have played successive away games at Manchester United and then Sunderland, who they beat on Tuesday.
O'Neill said: "It's interesting Arsene Wenger made the point that in what should have been a full Premier League programme some teams didn't play in midweek.
"I understand where he is coming from because some teams are getting an advantage.
"Stoke City didn't play this week and it stands to reason they would be fresher than us. I can understand what's been said (by Wenger).
"It should have been a full programme but it clashed with the Europa League.
"The Premier League should have had a look at that. Are those added few days' rest worth an extra few per cent? Absolutely, without question.
"But we'll just have to pick ourselves up and go again."
O'Neill has plenty of admiration for Stoke boss Tony Pulis and has warned his side to be on their guard at set-pieces.
He said: "That will almost certainly be part of the game and we have to be very careful at set-pieces. They will cause problems.
"But equally, I think they have added more quality to their team this season which has made them stronger. They will be a genuine handful."
Villa threw away a two-goal lead in the home draw with Stoke last season and O'Neill admits that was a crucial result when they were battling for a Champions League spot.
He said: "We played exceptionally well to go 2-0 up and we lost the lead and got a single point. It can happen. Arsenal drew recently 2-2 at West Ham from a similar position.
"But that result was definitely a blow to us and a few days later we were unable to raise our game in the first half against Manchester City."