For starters, the best explanation I've read for the numbers used in the formula is that they were devised using a matrix with run values for each play outcome. Maybe I just need a mathematician to explain to me how this is possible, but this seems to be an oversimplification of all the possible outcomes after a pitch.
Johnny Cueto has been knocked for having a lower ERA than FIP, but thats largely because he doesnt have high strikeout numbers. FIP doesnt take into account that when a pitcher is changing speeds and locating well, pitches that are hit are generally more poorly hit and easy to field.
It likewise doesnt consider the intangibles of the pitcher in question. If a pitcher gives up a walk and then a double that his RF lost in the sun, a really good pitcher can more often buckle down and escape the inning giving up one or fewer runs, a poor pitcher may let a misfortune like this open up the floodgates to a bad inning.
Lastly, it gives no consideration to how well a pitcher holds runners or picks them off. A pitcher with a slow delivery/bad pickoff move is giving the other team a huge advantage with their ability to steal bases.
In short, I feel there are plenty of good stats (classic and more modern advanced metrics) in place to judge a pitchers worth. Any one care to explain to me what I might be missing?