PSA: Phillies fans, read at your own risk.
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Depending on who you ask, the Phillies either cost themselves a couple of decent players or set the franchise back ten years in their transactions involving Cliff Lee. So often perception drives rhetoric, less often perception actually equals reality. Perception only equals reality with proper perspective, so let's attempt to gain it by studying the transactions, assuming no benefit of hindsight.
If you took the players the Indians have traded away in the past two years--two top-of-the-rotation workhorses and a switch-hitting, all-star catcher--you'd have the makings of a pretty good team. Lee was the second of the two aces dealt, and much like CC Sabathia he was crucial to his new team's playoff run. While Sabathia's 2008 brilliance down the stretch merely bought the Brewers a spot in the post season tournament, Lee was instrumental in his team's advancement to the tournament's final round. But it wouldn't be enough to overtake the Yankees, who ironically featured a rotation headlined by none other than Sabathia.
None of this was known at the time. What was known is the fact that Lee all but guaranteed the Phillies another division title and greatly improved their chances of defending their world championship. What was also known is the Phillies had to pay handsomely for Lee's services. If you're willing to consider Lou Marson and Ben Francisco a wash, here's what the quantification of the resources swapped looks like:


If since the strike there's been a more even swap, in terms of value, I'd like to see it. At the time of the deal it was considered a steal for the Phillies. It's true that the package the Indians received isn't as strong as that typically exchanged for a year and 1/2 of an ace, but more so because teams are frequently inclined to overpay in the midst of a pennant race, not because the prospects were worthless or bad. They might could have gotten more, but the deal absolutely made sense--for both sides.
Continued below.
Perhaps because locking up their ace long term was a priority, the Phillies made a curious and noisy trade two months after the 2009 post season, shipping another trio of prospects to Toronto for Roy Halladay and simultaneously shipping Cliff Lee to Seattle for a separate trio. There are a lot of moving parts, here, I've done my best to simplify it via visualizations. The resources, quantified:





As you can see, this is exactly the point where everything stops making sense for Philadelphia and turns into highway robbery. It's natural to question the thought process behind such a lop sided move, especially for the party that comes up with the short end of the stick. So, what the hell were the Phillies thinking?
I can think of a few possibilities. One, they over valued the extension they gave Halladay. With the extension in place, I have Halladay as a $25.6 million commodity through 2013. What I haven't displayed is his value had they not extended him, which is a quite similar $20.1 million. If you have a $7 million house with a $7 million mortgage, your house is worthless. If you lock up a free agent at market rate, you haven't gained very much. This is universally true. Parting with prospects for the privilege of paying a player market rate is foolish.
Two, they didn't know just how good Cliff Lee is. I have a hard time buying into this theory, given the Phillies excellent reputation with respect to scouting. Still, Halladay's contract over Lee's contract was nothing more than a wash, a redistribution of value (to their MLB roster) rather than an addition. Nearly all of the deficit can be explained by the difference in the quality of prospects exchanged. Why the Phillies thought Halladay and his extension was worth two top-30 prospects and a fringe top-100, but Lee was worth only a fringe top-100 prospect and two sub-100's, I have no idea, but that was the biggest mistake Amaro made in handling this situation.
Since then, things have only gotten worse. After three months with Seattle, Lee was traded to Texas along with unremarkable reliever Mark Lowe for Justin Smoak, Blake Beavan, and unremarkable (at least from a baseball standpoint) prospects Matthew Lawson and Josh Lueke. Smoak is a more valuable commodity than the trio Philadelphia received from Seattle combined. Quantified:


As if that weren't enough, the prospects the Phillies got for Lee haven't exactly set the world on fire in 2010. Aumont has walked as many as he's struck out in AA, Ramirez has been solid if unspectacular at the same level, and Gillies--hitting .238/.286/.333 in AA--is now being billed as a future 4th OF.
Start playing "What if?" and the Phillies fans you know might reach for a weapon. For instance, what if the Phillies had waited to move Lee and hadn't signed Ryan Howard for 5 years and $125 million, and traded Lee for the Smoak package last week, enabling them to keep Werth, rather than Ibanez, past 2010. You'd be looking at a 2011 line up consisting of Smoak, Utley, Rollins, Polanco, Domonic Brown, Victorino, and Werth, rather than Howard, Utley, Rollins, Polanco, Brown, Victorino, and Ibanez. Swapping Werth for Ibanez makes the line up infinitely less lefty-heavy (and, thus, LOOGY vulnerable) in the middle, and the difference between Ibanez and Werth likely more than accounts for the difference between Howard and Smoak.
Betting against the Phillies scouting and player development department isn't something I'd normally be inclined to do, but the route they took to now is inauspicious at best, probably costing the team something like $30 million in the process. Whether you view this as losing a couple of decent players or setting the franchise back a decade is your choice, but the argument that the Phillies handled the situation poorly is nearly unassailable.
The Phillies still have an excellent core and they could very well win this year, and next year, and the next, and the next. This was true before the Lee-Halladay thing went down, though, and if they'd handled the situation better, they could conceivably win more and for longer.
As always, all's not lost if knowledge is gained, and so long as Ruben Amaro and company have learned from their mistake, they'll probably soldier on, bent but not broken. If they make the same mistake again, though? Well that would almost certainly set the franchise back a decade, and might be enough to induce a few pink slips from the team's ownership.