Prospect valuation

There's an excellent article at BP about prospect valuation posted here:

http://www.baseballprospectus.com/article.php?articleid=4750

Here's the thesis:

Michael Bourn is a center fielder who played in the Eastern League last year. BA offers the following scouting report:

Bourn offers the quickness, aptitude and offensive approach required of a leadoff hitter. He's the system's best defensive outfielder and also has an above-average arm.

Here too, PECOTA largely agrees with BA's assessment. Bourn's speed scores are off the charts, and he rated as a +9 in center field last year. It doesn't think Bourn's a sure thing--his strikeout rates are high for a player with his profile, and he almost certainly won't develop home run power. But it gives him about a 25% chance of getting up to an EqA in the .265/.270 range, heavy on the OBP side and coupled with good baserunning, which would in fact make him an adequate leadoff hitter.
But how does Bourn rate compared to Shane Victorino, the International League MVP who will inherit the fourth outfielder's job in Philly next year? PECOTA would seem to have reasonable enough expectations for Victorino. It thinks he was playing a little bit over his head at Scranton last year, where he put up a .282 EqA, and pegs his 2006 at an EqA of .266 with plus defense in center field. It doesn't expect Victorino to get any better from here on out, nor does it see much in the way of star potential--his 90th percentile forecast only gets him up to a .289 EqA.

So we have:

A 23-year-old center fielder who has little star potential, but about a 25% chance of developing into a solid regular.
A 25-year-old center fielder who has little star potential, but who could be a solid regular right now.

Which of these players is the more valuable commodity? The answer to that seems obvious enough, and PECOTA's various long-term valuation metrics say that Victorino is perhaps two or three times more valuable than Bourn. But BA has Bourn ranked as the #3 player in the Phillies system, whereas Victorino doesn't crack in their Top 10 (in one of the weakest systems in baseball).

The A's farm system is frequently described as barren after the advancement of so many young players over the last few years, but I'm wondering if that is really an apt evaluation. Although the A's lack any high-ceiling prospects, it does seem like that have more than a few who promise to be regular contributors that the ML level. Dan Johnson may not be a Jason Giambi, but he's highly likely to give us 5 years of very solid production for league minimum.