The Britannia Stadium club fell to an opening-day setback courtesy of Andreas Weimann's winner five minutes into the second half.
Stoke, who handed debuts to Bojan Krkic, Mame Biram Diouf and Phil Bardsley, were unable to mount a fightback, and Hughes believes there is plenty of room for improvement.
"We expected more," he said. "Credit to Villa, I thought they came with a game plan and executed it well.
"We found it difficult to find the answers in terms of what we were trying to do.
"I thought we were the better team in that first half, created more chances, had more opportunities and, with a little bit more care with the final pass, I think we could have got the first goal.
"It's always important to get the first goal, especially at Premier League level because it's huge.
"Unfortunately, Villa were able to do that. Disappointing because it happened just after half-time when we'd spoken about the importance of it.
"From that point onwards it became easier for Villa to see the game out because they got people behind the ball, worked hard and made it difficult for us in the final third to be able to create anything.
"It's a wake-up call because there was a lot of expectation and maybe that's been tempered somewhat.
"Maybe that's no bad thing because we know it's a season where we're going to have to work hard.
"As a group we've never denied that, but we need to be better than we were."
