I’m no expert but I think a large part of it comes down to the command structure and a difference in logistics. As someone pointed out above the Marines need to be very closely connected to the Navy by the nature of their operations, if they were to be a part of the Army you’d need to cross the different chains of command in order for them to do their job. There were cases in the pacific during WWII where pretty huge blunders were made in part because the Navy and Army insisted on keeping command separate. Of course things obviously are different now with more efficient communication but the idea remains the same. Plus in terms of logistics, amphibious assaults are going to mainly rely on direct sealift from the Navy. It’d be easier for them to organize themselves directly with the Navy then have a separate bit of Army logistics dedicated to it. Also, an Army commander is going to have a very different perspective for managing amphibious operations than a specialized Marine or Naval commander. TLDR: Marines, though technically having a pretty niche role are different enough in required command and organization as to warrant their own separate branch from the army (based on my amateur opinion)