If the engines are put directly under the wing -- apart from the problems of cluttering up the airflow surface you also start to get problems with ground clearance. To alleviate this you would need longer landing gears which lead to larger gear bays and therefore more weight.
Have a look at the 737 - if you put the engine directly under the wing the landing gear would need to be extended by about 2 foot.
Another point is that with the engine so far forward it allows easy access all around the engine for maintenance.