As a huge fan of Pokemon and someone really invested in seeing the IP in the Orlando parks, I can't see how the series could top the visual wow-factor of the Poseidon's Fury facade and signage, or the acclaim recieved by Mythos' menu and service. I think both will be definite losses for IoA that we will not see matched again.
In basically every other aspect, I think Pokemon has the chance to deliver an exponentially superior guest experience than Lost Continent ever did across its' very long life. Near the end, Lost Continent was a collection of wildly cool facades, with nothing usable left inside of them.
I would love to see the few aspects of Lost Continent that remained appealing towards the end, like some of the visual elements, the area loop, and the Mystic Fountain retained in some form within Port of Entry. Other aspects seem to already be made up for; Mythos -> Thunder Falls, LC lore being consistently referenced in USF seasonal events, the Halloween shop and vendors finding a spot in Port of Entry. Given everything, you can't say UDX hasn't been paying its' respects to Lost Continent's legacy, and working to fill the gaps left in its' absence.