When aircraft become smaller, it is difficult to place engines under a wing and still maintain adequate wing nacelle and nacelle-ground clearances. This is one reason for the aft-engine arrangements. Other advantages are: Greater CLmax due to elimination of wing-pylon and exhaust-flap interference, i.e., no flap cut-outs. Less drag, particularly in the critical take-off climb phase, due to eliminating wing-pylon interference. Less asymmetric yaw after engine failure with engines close to the fuselage. Lower fuselage height permitting shorter landing gear and airstair lengths. Last but not least - it may be the fashion.
The center of gravity of the empty airplane is moved aft - well behind the center of gravity of the payload. Thus a greater center of gravity range is required. This leads to more difficult balance problems and generally a larger tail.
The wing weight advantage of wing mounted engines is lost.
The wheels kick up water on wet runways and special deflectors on the gear may be needed to avoid water ingestion into the engines.
At very high angles of attack, the nacelle wake blankets the T-tail, necessary with aft-fuselage mounted engines, and may cause a locked-in deep stall. This requires a large tail span that puts part of the horizontal tail well outboard of the nacelles.
Vibration and noise isolation for fuselage mounted engines is a difficult problem.
Aft fuselage mounted engines reduce the rolling moment of inertia. This can be a disadvantage if there is significant rolling moment created by asymmetric stalling. The result can be an excessive roll rate at the stall.
Last but not least - it may not be the fashion.
It appears that in a DC-9 size aircraft, the aft engine arrangement is to be preferred. For larger aircraft, the difference is small.
An aft fuselage mounted nacelle has many special problems. The pylons should be as short as possible to minimize drag but long...