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While there's a ton here to applaud, I think you buried the lead, (at least, the Lead IMO).
"... Felix had a 4.52 ERA as a rookie ..."
Let me add, (though a diametrically opposite pitcher type) ...
"Greg Maddux had a 5.61 ERA as a rookie."
To me, those two statements are HYPER-critical when discussing rookie pitchers.
Based on everything I've seen, read, heard, etc. - I'm convinced ... Pineda has a 90% shot at becoming an All-Star TOR pitcher.
I also happen to believe that he's more likely than not going to be posting an ERA closer to 5.00 than 3.00 as a rookie, (as Felix and Maddux both did).
While there are occasional rookies who come in and post sterling numbers from day one, my sense is that most of these end up going through their own "rookie season smackdown" somewhere down the line.  I believe it's just a case that pitching is simply different than hitting.  I think pitchers have some things about their craft that they can *ONLY* learn through experience. 
I think you (and Pineda) nailed it when noting he threw too many strikes.  And there's the crux of the problem.  Against lesser competition, you CAN throw strikes every time you want and not suffer (badly) for doing so.  Against MLBers, it's a different story.  KNOWING this is a problem is only the first step.  But, only through experience, (of getting too much of the plate), will Pineda find the optimal time/situations where nibbling is the superior choice.
A guy like Cliff Lee *can* walk very few hitters.  But, years of experience are what ALLOW him to walk so few hitters. 
What's funny about Felix is, it "looks" like he had this incredibly smooth and linear improvement, (his ERA goes: 4.52; 3.92; 3.45; 2.49; 2.27).  But, when he arrived he walked only 2.8 then 2.5 guys per game.  Then, in 2008 that jumped to 3.6.  It "looks" like just a bad year, since he dropped back down to 2.7 and 2.5 in '09/'10.  I think it's MUCH more complex.  He HAD to walk more guys in 2008, because he understood he was allowing too many HRs.  And his HR rate did drop slightly in '08.  But, it was in '09 that he finally figured out the situational aspect -- where he could intuit when to be aggressive and when to be passive.  The result was a lowering of BOTH his walk and HR rates. 
The Atlanta Big Three were stupendous at HR prevention.  They all three had drastically different styles and stuff -- but each could execute THEIR staff on demand.  But, what made them great was they avoided the mistake pitches for 15 years. 
The likely reality for Pineda is that "as a rookie", he is not going to avoid the mistake pitches.  He, (like Felix and Maddux), is probably going to have a year of failing to live up to expectation - though he'll likely have some individual killer games along the way. 
It's the difference between throwing and pitching.  Pineda probably has the ABILITY to become a Hall of Fame pitcher.  It is the mental side ... how he reacts to the mistakes ... how he adjusts his game and learns along the way that will determine whether he gets there or not.
A 3.20 ERA would be wonderful.  But, a 5.20 ERA should not be considered a death knell.  The most important aspect of player DEVELOPMENT that the fans need to keep in mind is that instant gratification should not be the expectation.  At best, one can hope that the growing pain period is short.