Ships are the only way to transport and deploy certain weapons across theaters; as such, there is no simple way to replace them. Your argument could be made in the era of Soviet anti-ship cruise missiles (and that argument was made), yet navies have continued to develop and deploy warships.
That is unfortunately a complicated trade off, involving initial construction costs, total capability, maintainability, and crewing costs. Simply put, two amphibious assault ships do not equal or supersede one super-carrier.
