Well, Chuck said it best, but I'll add this: You
get fewer components,
 lower cost, easier maintainability and tweakability, increased
 flexibility, the possibility for a reusable design...how is this a bad
 thing? 
 I question the over head ... with all the design software closed source
 I bet Mr Gates has control of I guess 75% of your hardware product. 
 
     I know no microcontrollers that hasn't unix/linux tools, nor one who
 doesn't is documented - programming algorithm, asm and like.