Ideally, I'd have MSHI expanded out to that area with something new. I'd actually go for a whole modern redesign of MSHI.
For a sit down restaurant, I'd go high end and stick a Winston's Steakhouse in Jurassic Park/World if they ever feel the need to upgrade JPRA and finish updating the area.
jurassic-pedia.com
As for Toon Lagoon, I don't know what I'd do. I think the whole area needs redone.
Popeye's is the greatest version of a river rapids ride and I'd be sad to see it go. Dudley's is in bad shape theming wise but the barebones of the ride is fantastic.