Lengthening muscles not good from evolutional perspective? Why do we do it with explicit stretching?
Muscles only ever work by shortening, as you say, but muscles in the human body tend to be found in antagonistic pairs.  These pairs of muscles act in opposite directions, one example being the biceps and triceps muscles - the biceps bends the arm (a flexor muscle) while the triceps straightens the arm (an extensor muscle), another example is the quadriceps-hamstring muscle pair in the upper leg.  

If our muscles remained shortened, our mobility would be impaired.  If the biceps muscle remained too short, it would be impossible to extend our arms, for example.  Muscles do work by shortening, yes, but it's important for them to be able to stretch as well, and remain long enough for antagonistic muscles to have their full movement be possible as well.