He has injury problems and marchisio is better. Marchisio can play regista at a top level, something Bayern have a lacking in at the moment and he can play as B2B. Khedira can only do the latter and is injured most of the time.
Fast forward six months and we'll hear people suggesting to get rid of another injury ridden player. People on here are so ruthless when it comes to injuries.
I've just recently started training again after my ACL injury and always feel so bad when someone does his knee.