I think a special bat has a lot more value than a special glove. Even if Soto looks like a defensive liability, his bat probably means he can be dealt for something more valuable than a plus plus CF who we hope will scrape together enough of an offensive game to stay in the line-up. That CF is Corey Patterson if he can't play on the offensive side.
I was impressed by Stubbs progress in 2008 as well and I have him at number 4, but Frazier, Alonso and Soto are clearly a cut above the rest of these guys IMO.