The process in IST is clear and follows a standard procedure. This is valid for the 737 and the Airbus. The procedure for the 777 is painful as there is no sim in IST and a complete communication lack (as it seems) between upper management and OPS about fleet requirements and the need of speedy integration of new people exists.
was sitting in IST for 3 weeks to wait until they got the act together
Now this is most probably not even THYs fault. While the residence visa can be issued in one day (I saw this happening in about 4 hours), the working permit takes weeks to be processed.
However, the support and / assistance for crews arriving for screening lacks any professional standards. THY has to change attitude towards the non-Turkish crews and play as an international airline as they claim to be.