To streamline the process and for different mission sets. Take the Navy for example. They have fighters like the F/A-18 that has to be able to take off and land from an aircraft carrier and perform air to air and air to ground combat missions. A carrier capable aircraft needs very sturdy landing gear to absorb the harsh landings at sea and equipment to launch from the catapult. It also needs special materials to be corrosion resistant. An Air Force F-15 doesn’t need any of that and it would be wasteful to incorporate it. The Marines are a bit strange as they are under the department of the Navy and are closely associated with them. However the Marines have a more particular mission of being an expeditionary force that will fight on land wherever they are needed. To support those troops requires their own smaller Air Force that they have control over.
By splitting up the branches and providing them with their own aircraft they can specialize on their own missions and their own funding.
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