Predecessor Tony Pulis was sacked at the end of last season after taking Stoke as far as the club's hierarchy felt he could, and with chairman Peter Coates wanting to push City in a different direction.
Despite five consecutive seasons in the top flight, a number of cup runs and a Europa League adventure, Pulis failed to attain a top-10 league finish during his tenure.
It has now fallen on Hughes to take Stoke to the next level, only for the Welshman to suffer continual frustration in his bid to strengthen the squad this summer.
Hughes has only signed defenders Erik Pieters and Marc Muniesa, along with bringing in forward Oussama Assaidi on loan from Liverpool.
With the window closing at 11pm on Monday, a disappointed Hughes said: "We would have liked to have done more business to this point.
"But it's been more difficult than most windows. We've pursued a number of targets, got so far with them - and in some cases we were very close - but then all of a sudden it just fell away.
"They've not been for the same reasons, but very different reasons, with regard to almost every one of them.
"That's been frustrating because you put in a huge amount of work, try and get everything in a line, you think you've done it, and then all of a sudden a piece (of the jigsaw) doesn't correctly fit, and it can't be done.
"That's what we've experienced this window, although we're still hopeful."
It means to break into the top 10, Hughes will have to go with a squad for the most part shaped by Pulis.
Despite that, Hughes sees no reason why Stoke cannot make the breakthrough into the top half of the table this season.
"I've a good group of players, but we do need a little more help in terms of that group and the type of players I want to bring to the club if I can," added Hughes.
"If that's not possible then we'll still have a group that has the capability of doing well in the Premier League again.
"It's going to take some time - it may take more time, may take less than I think - but the intention is to be a successful top-10 Premier League side on a regular basis.
"That hasn't been the case in the past, and that's the challenge for every one of us.
"Ideally, to be a recognised top-10 Premier League team, we have to embrace a different way of playing, and if we do that then we'll keep on progressing."
Despite suffering an opening-day defeat at Liverpool, City have bounced back with successive home wins over Crystal Palace and Walsall, the latter in the Capital One Cup on Wednesday.
The Potters now face a so-far unbeaten West Ham at Upton Park on Saturday, with Hughes expecting a positive result.
"We have been encouraged by the way we have played, although we all feel we can play better," said Hughes.
"But confidence comes from winning games, and that's what we've gained from back-to-back wins, so we're pleased with that.
"We also went to Anfield and caused Liverpool problems, so there is no reason why we can't put in the same level of performance.
"If we do that then maybe we'll have a little more luck and come away with some points. That's the challenge for us, to get three wins on the bounce."
After his hat-trick against the Saddlers, Hughes must decide whether to give Kenwyne Jones a start, or recall Peter Crouch after he missed the midweek game through illness.