Paul O'Connell's return to fitness late on in the season was crucial to their march to the Heineken Cup semi-finals but the 33-year-old was sorely missed in the RaboDirect PRO12, making just four appearances.
O'Connell remains a key part of Penney's squad but fly-half Ronan O'Gara - another integral cog in the club's golden generation - has left as Munster, under their Kiwi coach, set about continuing their new era.
Doug Howlett is another club stalwart to leave this summer - due to retirement - but in Simon Zebo Munster have another flyer ready to take on the mantle.
And flanker O'Mahony, who at 23 became the youngest Ireland captain this summer since Brian O'Driscoll, believes the signs are good for the new campaign.
'It's coming together well, it's Rob's second season now," he said.
"We've got a couple of good building blocks set from last year, very good performances from the end of last season.
"It's exciting, very positive and I think everyone's looking forward.
"I think we had a couple of teething problems [last year] particularly in the middle of the Rabo and the games that we would have won a couple of years ago we were on the wrong side of which was disappointing.
"And that's something we'll definitely be concentrating on this year to improve, get a bit more consistency and good performances.
"We weren't happy with the way it went and we weren't happy with where we finished in the table so we'll be looking to improve there big time this year.
"That was unfortunate. We had a decent start, it was just that middle bit. Just games where Munster normally kick on, win by a point or two, we ended up on the wrong side of which was the disappointing thing. We'll have to address it this year.
"I do [think the squad is stronger]. We have a couple of great athletes with huge ambition. They'll all be looking to get a starting place to make it theirs."
And while O'Mahony is determined to see Munster improve their form in the RaboDirect PRO12, he's also hoping for another European adventure this season.
"The Heineken Cup is where we judge our standards and the Rabo is where our bread and butter is done," he added.
"We have to perform week in week out.
"We were reasonably happy with how the Heineken went but we were obviously heartbroken after that semi-final.
"It could have gone either way, maybe a little bit more self-belief from us could have kicked it on a bit. We probably didn't perform well enough in the first-half to end up winning the game but the last two or three performances in the Heineken were positive for us and something we'll be building on for this season."