What you are doing is very consistent with some of the best baseball statistical research being done these days. That research shows that things like ERA and WHIP are heavily influenced by the fielders behind a pitcher, ballpark factors, and random things that the pitcher cannot control. The things that a pitcher has much more control over are K/9, BB/9, and HR/9. I use those almost exclusively to rank pitchers, then toy with my rankings based on assessment of team defense, ballpark, strength of the offense, etc.
If people are interested, I can post some links to the guys that are doing the research. Voros McCracken is one guy that you might have heard about.