I agree with most of what you said but I just wanted to make a point on this part. What's stopping Shark from performing to his peripherals is HRs. He had 13.3% HR/FB ratio last year and a 12.8% in 2012. IF you look at his xFIP which uses a base 10.5% HR/FB(believe this is the league average) his ERA the past two seasons would have been 3.38 and 3.45. That would have made him tied for 37th among qualified pitchers last year in ERA and tied for 22nd in 2012. You're basically talking about a fringe #1. He'd probably be in the conversation for top pitchers 15-45. Some where in that mix.
His HR/FB% over his career at Wrigley is 12.1% vs 10.2% on the road. So its fairly evident that playing in wrigley is hurting him in that regard. If he were traded to a team with a bigger OF his ERA would likely drop quite a bit. For example, he has a 1.76 career ERA at PETCO in 15.1 IP, 2.57 at Safeco in 7 IP, 0.76 at PNC in 35.2 IP, 2.84 at AT&T in 6.1 IP, 3.45 at nationals park in 15.2 IP, and 5.91 in Busch in 21.1 which were all HR unfriendly. That's 30 ERs in 101.1 IP or 2.66 ERA. Is that cherry picking? Perhaps, but it illustrates the point. Contrast that to his 3.87 in 228.0 IP at wrigley and you see a tale of two different pitchers.
In that light, I'm glad this front office realizes his value and wasn't willing to just toss him away for whatever they could get.