Why use JK flip flops when D flip flops are simpler?
The simplest answer is that D flip-flops are MORE complicated than JKs. Logically, a D FF is a JK FF with an extra inverter between the J and K inputs, like so







simulate this circuit &ndash; Schematic created using CircuitLab

while converting a D to a JK requires much more logic (which I am too lazy to draw out. Trust me.)

so conceptually a JK is simpler by one gate. Of course, this may not be reflected in actual transistor count, but I'm not an expert on IC design.

And while it's true that the two can be made equivalent with some extra gates, some logic functions require fewer external gates depending on the desired function. It all depends.

If your underlying question is, "Why do they make us study JK flip-flops when D FFs are simpler?" the answer is that JK FFs are more versatile, specifically because of the more complex logic table. 

And finally, you have the historical sequence wrong. JK flip flops were produced before D types due to their more general nature. For instance, in the classic 7400 TTL series the first flip flop is the 7470, a gated JK. The first D type is the 7474, although eventually that eclipsed other types.