Slowly but surely, however, things have begun to turn around under the guidance of general manager Neal Huntington. In 2008, the year after he took over, Baseball America ranked the Bucs' farm system 26th in baseball. Now, it ranks seventh.
And while it's still been two decades since the Pirates have had a winning season, the consensus in the clubhouse is that the organization has never been deeper, and there are now more Major League-ready players waiting to seize opportunities.
And Mercer's May is a perfect example.
"We played a stretch in May without [Russell] Martin and [Neil] Walker, and we were able to hold fast and win games," said Pittsburgh manager Clint Hurdle, whose team is 11-6 this month. "That speaks to the depth, collectively."
Mercer, a middle infielder, spent nine days with the Pirates earlier this month when Walker went on the disabled list. He hit .258 with four RBIs, three home runs and five runs scored in 31 at-bats in that stretch. Mercer was then sent down on May 13 when Walker returned, but he was recalled less than 48 hours later when John McDonald landed on the 15-day shelf, and Mercer remains on the active roster.
"It's a challenging task, but it's another sign of our organization getting better," Hurdle said of having to send Mercer down. "More often than not, when you're on a good team, you expect the players to come up and to perform well. And when they fill spots for regulars, you feel confident in the development system."
Mercer stepped in on Wednesday, the same day he got back to Pittsburgh, and went 1-for-2. But when everyone is healthy, there's just not enough room for guys to stick around for long, no matter how well they play.
"It's a good problem to have," center fielder Andrew McCutchen said.
And traveling that much in a short period of time, like Mercer did, is never easy on a player.
Focusing on family, travel and playing a Minor League game, all while hoping for that phone call from the Pirates, is a challenge. But it's a challenge Mercer is more than happy to face.
"This is the big leagues, and I keep telling myself that," Mercer said. "This is where you want to be, and this is the ultimate dream, ultimate goal. And nothing is better than this, so it doesn't matter if I haven't slept for a week."
One of Mercer's two teams this year, the Triple-A Indianapolis Indians, has been dominant in the International League the past two years. The 2012 club had a league-high 89 wins with just 55 losses, and the Tribe is off to a blazing 31-14 start in 2013. The 26-year-old has batted .333 with 19 RBIs and 11 runs in 26 games there this season.
Of course, Triple-A isn't as much about winning as it is about contributing to the overall success of the organization.
Indians manager Dean Treanor tends to the difficult juggling act of putting a winning team on the field while developing talent and preparing players who are champing at the bit to get to the big leagues.
"Everyone in this tier knows they're a phone call away," Treanor said.
Mercer has been just a ring away pretty much all season, and made the most of his opportunity.
"He added value to us, and he added value to himself by being up here," Hurdle said after Mercer was sent down. "And he's walking out with a better understanding of what kind of player he thinks he can be."
Hurdle and Treanor both said part of what makes the quick transition from the Minors to the big leagues so smooth and effective in the organization is the relationship the two managers have established.
Treanor said he's never worked with a manager more invested in his Triple-A club than Hurdle.
"It's not even close. It's the best relationship I've had," said Treanor, who has been coaching at the Triple-A level since 2002. "It's a genuine interest in how guys are doing here."
The two managers talk at least twice a week and give each other the full rundown of their clubs. Their phone call Wednesday lasted about 45 minutes.
Hurdle has plenty on his plate, but he doesn't see that as an excuse to leave his Minor League managers in the dark.
"If it's truly about the organization, you find time," Hurdle said. "Nothing but good's going to come from it."
And Hurdle, who's managed at both the Triple-A and Double-A levels, has seen both sides of the spectrum when it comes to communication between different levels of management.
"I've been a relationship where it's healthy, and I was spoken with and asked a lot of questions," he said. "And I've been in a relationship where I felt like I was out on an island. I was never talked to. So I know the difference, and I know the feelings that can go with both of those."
In the end, however, that behind-the-scenes communication will always go unnoticed by fans and critics.
What's important is the product the Pirates put on the field, and if that product doesn't pan out, no one will care about how deep or effective a Minor League system the Bucs continue to construct. The losing season streak will still be the focus.
"We're here for the Pirates," Treanor said. "That's what all these guys are here for."