Despite an unconvincing home win over Hull last time out, which followed a 3-2 defeat at Cardiff, the Chilean chose to make six changes to his starting line-up for Saturday's Premier League clash at the Britannia Stadium.
Pellegrini was clearly holding some players in reserve for the Champions League Group D opener at Viktoria Plzen on Tuesday night.
As a result, City were distinctly below par again and Stoke looked the more likely side to win - but Joe Hart denied Kenwyne Jones on more than one occasion to keep the scoreline blank.
When asked about Pellegrini's rotation policy, former Etihad Stadium manager Hughes said: "You need to know what the Premier League is like.
"It's unforgiving and no game is easy. You can't really place one game above another because you can come unstuck.
"Very rarely do you get teams from the bottom beating the top (abroad) but in the Premier League you always have examples of that, and that's why everyone watches it.
"That's a balancing act that Manuel Pellegrini will have to cope with. It's not easy, but he has got great riches there in terms of talent."
Hughes acknowledges the Champions League is taking on ever more importance for Manchester City as they seek to reach the knockout stage at the third time of asking.
"I think the progression is there for everyone to see," said Hughes in the Daily Mail. "They have won every cup and gone on to actually win the Premier League, but the one thing that they have not been able to make any progress in is the Champions League.
"It's probably the one stick that people can use to hit them over the head with. I suppose that is the basis on what they will judged by this year because of their lack of success in it so they will be looking to do better in the Champions League this year, I'm sure."