A youthful Rovers side down on numbers went behind to Tom Ince's tap-in late in the first half with Sam Surridge's third goal in a Stoke shirt sealing victory for the Potters.
But on a night when they were missing a number of senior players, Rovers' passing football delighted Wellens and augured well for the future. The result did not tell the whole story, in his view.
He said: "I thought some of our young kids were outstanding. You look at the average age of that squad, Ben Blythe, Branden Horton and obviously, we made a change with Charlie Seaman coming on and (there were also) Matt Smith and Aidy Barlow.
"There were so many positives and really good performers. In the big moments, they showed their quality and we hit the first man with too many crosses.
"When they get in wide areas, they (Stoke) whip it in, miss the first man and put it in dangerous areas. But I think, if you take both boxes out, we were better than them. I thought our rotations were good and we passed the ball really smoothly.
"It is just in both boxes where they were physical in the defensive one and they got some real quality at the top end of the pitch."
Rovers may have done it tough in terms of results and player unavailability so far this term during the early part of Wellens's tenure, but the Doncaster chief is steadfastly looking at the bigger picture, which he believes is rosy.
Wellens, who did not include striker Omar Bogle in his squad, with the Rovers boss hoping to move him onto pastures new, continued: "My remit is to get an identity back and I looked at the team and they were well coached with a clear identity of what they want to do.
"I will continue to make decisions for the long-term benefit of this football club because my plan is to be here long term.
"I can make decisions which for the short term might be better for me, sometimes I am cutting off my nose to spite my face, I get that.
"But I will make long-term decisions for the benefit of the club to get its identity back and get long-term sustainable success.
"I absolutely hate losing, but there were some really good performances from the young lads and they can take big confidence from it."