I decide to take the suggestions to have Angel and Fluttershy have a kid.  
because ideas
 
Basically, the few pony scientists around finally realized a sort of cure they could work around. Having a child with another species could result in carrying the foal to full term. Some ponies experimented with turning animals into half-pony like creatures (some which escaped, uninfected with the “curse” an able to breed freely) and others mated with Crystal Ponies, Dragons, etc. This “cure” came about years after the main six had their children.
 
Fluttershy was one the few who helped Twilight try to find a way around the curse, and ended up having a half-rabbit, half-pony filly named Cotton Tail. Cotton Tail is a very demanding, very assertive filly taking all of her cues after her “father”. Cotton always finds a way to take advantage of her mother’s kindness and is always causing trouble amongst the school yard. But she can also be very kind, in a backwards sort of way, secretly caring for those she takes advantage of.