Yes, player values do change over the course of a season. How much would teams have bid for Masterson or Craig as free agents last offseason? How about this offseason? If Lester had duplicated his first half of 2013, or his second half of 2012, or his first half of 2012, you'd feel much differently (well, OK, that's not fair. Rational people would feel much, much differently.) And, note that this was part of the evaluation -- 4/70 would have been a massive overpay for the Lester of 2012, right? So there was certainly some amount of belief that the second half of 2013 might be real, just not a willingness to give Lester a long-term major deal on the assumption that the second half of 2013 was entirely indicative of what he would be going forward.
Let's think about this one further a bit. Let's decide that if Lester's last half of 2013 is real, he's worth 6/135 to the Sox, their top offer. If Lester's first half of 2013 is real, or his 2012, he's worth...about 1 WAR/year and declining from there, so at $7M/WAR, let's say that he's worth at most about 6/30, and by the end of that you might not want him holding a roster spot. We can debate exactly how you should deal with risk, but let's just take expectation value here. We think 6/120 might have been what was necessary to get it done. So, if we decide that it's entirely boom or bust, you'd have to be 86% certain that his last half of 2013 is the part that's real in order to offer him 6/120. If I offered you a bet on Lester's 2014, at odds 5:1 in my favor, would you have bet that he would do at least as well as the last half of 2013? I can't believe that you'd have made that bet.
If we take the Cubs offer as what the Sox "should" have offered here, and nobody on this board seems to, then you'd still have needed to be 72% certain in order to make an offer of 6/120, and again, that's a sucker bet. However, if you feel otherwise, I'll offer you this: in 2014, Lester had a combined 4.8 WAR. If Lester tops 4.8 WAR in 2015, I'll give $28 to the Jimmy Fund. Otherwise you give $72 to the Jimmy Fund. I'm guessing you won't want to take that bet, and I certainly think the odds are stacked in my favor. But, I'm happy to make that bet if you'd like.
Similarly, the question about Cespedes, while still up in the air, isn't whether trading for Cespedes stopped us from getting Lester back. We didn't want him back at this price, and the Cubs would have made their offer anyway. The question is whether Cespedes is more valuable than a combination of having Lester for an extra couple of months last season instead of Cespedes (probably a negative, in that this way we found out more about our younger pitchers and got a better draft pick) and the compensation pick we would have received. We'll see what the final return ends up being, but I believe that one year of Cespedes is likely a better return than the average compensation pick (which we'd have lost when we signed Ramirez/Sandoval, so I guess it really would have given us an extra third round pick, but with a different offseason approach, it would still be a compensation pick). And, I believe that if we trade Cespedes, we'll end up trading him for something that's better than the average compensation pick.
So I really don't see the mistake here.