The missing option, in fact the view toward the future, is the presence of drones, not only for reconnaissance, but as combat vehicles.
Consider: Sortie rates could be met, in part, by UAVs for the fleet's eyes, and with further development, area control in tandem with manned fighters acting as the coordinating ship, in terms of mission adaptability and defense. Similarly, those UAVs could be developed with an offensive capability and not just a surveillance capacity.
That was not mentioned. Perhaps that capability could be combined with the well deck ships missions, not just for amphibious operations, but adapted to littoral combat as well, with a fleet of air and surface drones, and manned offensive vessels on the order of the old PT boat, with enhanced weapons packages.
Think smaller, faster, harder hitting, with support/launch/recovery/"mother" vessels being the larger ships.
Jefferson met much of our naval needs with deployed coastal gunboats, often kept onshore until needed, and this would project that concept much as the aircraft carrier projects air power, and possibly do so on budget.
If big targets are to become a liability having too many eggs in one very expensive basket, and being too expensive, that modification might make a force more viable in conflict.
I'm just a scientist, not a naval architect or tactician, and have not served in the armed forces, just read about it, so discussion is welcome.