Why design speeds are different?
Not a simple question to answer - I'll do my best to keep it understandable.
As ever, it all comes down to the bottom-line - MONEY
Think of the process as being like Cost Index - but you can change the plane design, rather than just the flight speed
The faster you want a plane to fly, the more wing sweep you need which starts to hit L/D, increase structural weight, needs bigger engines although engine SFC is reduced (can also impact noise).
All of these increase fuel burn per seat. Increased weight also puts up other costs like landing and navigation fees among others
On the other hand, reduced flight time can reduce time based costs like flight & cabin crew as well as maintenance costs. Further, more speed can increase aircraft utilisation permitting finance charges to be amortised over more flights per year.
I also believe there used to be an advantage in the old travel agents booking system that gave priority to the shortest flight times (faster aircraft) - unsure if this was/is true.
Clearly, there is a balance to be struck, and this is often influenced by the conditions at the time (fuel price, labour prices).
A couple of extreme examples
Concorde was an all out speedbird with little regard for fuel costs. If you like, this was largely an Airbus aircraft (similar partners apart from the Germans) and that was twice as fast as any Boeing aircraft. However, speed was not everything and the economics of the 747 eventually ran out the winner in terms of aircraft sales.
Boeing's Sonic Cruiser also pushed the cost of time vs cost of fuel issue but failed to converge to an acceptable solution.
Hope this helps