FIP is a flawed stat. It doesn't take into account groundballs and DP's. Plus, Lannan has shown an ability to outpitch his peripherals probably because he is a good pitcher when men are on base. Stammen does have a good WHIP, but he allows too many HR's and a high percentage of his hits allowed are Extra base hits. Not to mention that Lannan has shown he can throw 200+ IP while Stammen hasn't
ERA is a much more flawed stat as it doesn't take into account the quality of defense behind the pitcher. Lannan would be a solid back of the rotation starter on a great defensive team, but if you have better options, and we do, you don't leave a guy out there who can't K batters, BB a higher than average amount and gives up 1 HR/9.
Of qualified starters last year Lannan was 66th of 75 in BB/9, 75th in K/9, 36th in HR/9, 52nd in WHIP, 38th in ERA, 65th in FIP, 67th in ERA/FIP differential (meaning only 7 pitchers had a larger gap between ERA and FIP).
He's a young innings eater and nothing more. There's only so long you can tempt fate with pretty mediocre numbers that are better than they should be. If you can role out 7-8 guys with better talent, keeping Lannan in the pen for spot starts and injury coverage, then you do that.