I think there are many reasons why Miles is still around. First being that he is a popular character, one of the breakout stars of the Ultimate Universe so it makes sense that he would make the jump the main 616 continuity.
But I'm not sure how you can say that Peter as the original exists in a reduced capacity. Miles stars in his own book and is a member of the Avengers. Peter also stars in own book as well as the period book "Spidey" has a ongoing team up book with another popular character Deadpool and is a member of the Uncanny Avengers. Seems to me that Peter Parker exists in a much bigger capacity than before and certainly has more focus than Miles.