Galway's championship season was again ended by the Shannonsiders at the last-four stage of the Liam MacCarthy race.
In a game where the Tribes were outstanding for the opening 25 minutes, building up a six-point lead, Limerick's power play came to the fore therafter as they went on to record a nine-point victory.
Four weeks previously, Shefflin's side looked like ending a five-year wait for a Leinster title, only for Cillian Buckley's last-gasp goal denied them at the death.
Assessing those losses, Whelan, who was named PwC GAA/GPA Player of the Month, told RTÉ Sport: "We went in at half-time against Limerick in a decent position; we felt we could have been in a better position. We went out in the second half feeling confident but we lost some momentum and they got a run on us.
"Limerick are an absolutely outstanding team, massive credit to them on the day and it's something we'll spend the winter coming to terms with."
As for the heartache against the Cats, the Kinvara clubman added: "Any time a goal like that goes in you'd be disappointed. We don't have anyone to blame only ourselves. A goal that was one in a 100 but it's not something I'd dwell on as much.
"We had three or four chances before that to extend it to a four, five-point game. That's the winning and the losing of the game. In every game there are periods where you have a purple patch and then the opposition has a purple patch.
"We're still very much a team in transition and that day was a massive learning for us. We have to learn to maximise our purple patches and then try to minimise the opposition as much as possible. It's something we'll have to focus on going back next year."
In expanding more on the transitionary phase, Whelan referenced the likes of Johnny Coen, James Skehill and Aidan Harte, who are no longer around.
"We are going through a period of transition. Certain lads have passed on the baton. The challenge at the moment is to bed in the younger lads coming through, showing them the level it takes to compete against a team like Limerick. That's a job that is in its infacy.
"I think people have understimated the job that Henry has had to do."
Whelan, has every faith that 'King Henry' can successfully do the that job.
"He's a real leader. He's obviously had an incredible career. He's very good at working with players. For me as a forward, he's someone who I grew up watching and aspiring to be like. I find him very personable in terms of helping me to improve as a player. He demands massive standards, and giving it your all. They're all attributes that every manager asks for. We've massive faith in Henry and belief in him."
As a player who has faced Sunday's All-Ireland finalists this season, Whelan is well placed to give his opinion on the respective camps.
"Both teams bring different challenges. Kilkenny are massively physical. They have TJ, Eoin Cody, and Martin Keoghan up front. TJ is an absolutely amazing hurler who nails all his frees and then you have Eoin Cody who is in the form of his life as well.
"You have other forwards around them then working really hard. Defensively you're not getting much off them."
"Whereas Limerick would have different players stepping up every day and they're very measured in everything. I actually think it'll be a fascinating battle to see how that plays out. I was up at the final last year and it was one of those games where it was tit for tat and that's how I see it playing out again on Sunday."
"We've seen some slippages this year in the Munster championship: Clare beating them and Tipp getting a draw. On any given day teams can give them a game. It's just that when the chips are down Limerick have found answers. You have to give them massive credit for that.
"It's hard not to edge towards Limerick considering they have the three-in-a-row done and the way they came through Munster. You'd be very foolish to be writing the Cats off. I think it will be a very, very tight game, maybe Limerick to shade it, but it will be fine margins."
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