Most of the times, we need a flip-flop for storage.
D flip flop is the simplest flop that is available. Just a storage flop.
Eg:
1. It is not efficient to use JK Flip flop for shift register operation. (This is what is required at majority of the places)
2. However, there are some counters that use the J-K Flip flops to reduce external hardware. Remembering the Q(t+1) = JQ'+K'Q, JK Flip flop can be used where this feature makes the circuit overhead simpler.
This is my understanding.