Which of these players is more valuable right now: Jim Thome or Nick Punto?
It's easy to say Thome. He's a 5-time All-Star, 4 times finished in the top 10 for MVP, and is a likely Hall of Famer thanks to his 564 (and counting) career HR. The .847 OPS he put up last season was his worst since he was a 21-year-old breaking in with the Indians back in 1992.
Punto, even at his best in 2006 and 2008, could only manage a .726 OPS. His execrable hitting in 2007 (.210/.291/.271 in 536 PA - the worst production in the Majors that year by nearly .050 points of OPS) is seared into Twins fans' memories, as is his costly baserunning gaffe in the playoffs last season.
However, it is becoming increasingly clear to both fans and front office people that there are more ways to help a team win than just by hitting. Preventing runs in the field and moving around the bases are also important. The complete player possesses 5 tools: hitting ability (used to be just for average, though I think OBP is a better measure of this now), power, speed, sure-handedness with the glove, and strength and accuracy of the throwing arm.
Thome, at this stage of his career, is a 2-tool player: he can get on base, and he can hit the ball a long way. He is only capable of playing 1B, but has played just 28 innings in the field since returning to the AL in 2006. Could he score from 2B on a single? The ball would have to be hit awfully softly to an OF with a terrible arm. His effectiveness is severely limited against LHP, with a career OPS of about .750. Basically, all Thome is good for these days is mashing RHP as a DH or PH. Despite hitting 58 combined HR, Thome has been worth 3.5 WAR over the past 2 seasons according to Fangraphs.
Punto is a 3-tool player: he plays average or better defense at 2B, 3B and SS, his arm is good enough to play the left side of the IF, and he's a 75% base stealer for his career. When would he not score from 2B on a single? The ball would have to be hit awfully hard to an OF with a terrific arm. Though he struggles to hit for average and has no power, his career platoon splits are essentially equal, making him no worse an option in the lineup vs. LHP or RHP. His career BB rate of 9.9% indicates that he is at least a fairly patient hitter, helping to wear down opposing pitchers when he's in the starting lineup. Despite his offensive shortcomings, Fangraphs rates Punto as worth 3.8 WAR over the past 2 seasons.
Punto's versatility is a huge asset. In this era of 12-man pitching staffs, managers need to be able to get maximum flexibility out of their bench players. Punto can give rest to Orlando Hudson at 2B, JJ Hardy at SS, or Brendan Harris at 3B. He is now the most likely backup in CF when Denard Span needs a day off. On the days he doesn't start, he can PR for everybody on the roster except for Span and Alexi Casilla and be an upgrade on the bases. He can give a decent AB as a PH against any type of pitcher. And he can fill in at any of 6 defensive positions depending upon who else has been substituted from the game.
It's a nice luxury to have a guy like Thome on the roster. But a guy like Punto is a necessity.