Quick armchair Imagineering. If we roughly consider Toy Story Land and Star Wars Land to be a “Phase One” of Hollywood Studios being “overhauled,” this is what a hypothetical "Phase Two" should look like, in my opinion.
I think the park would be in fantastic shape after all that. Most of it is unlikely to happen, however!
For Animation Courtyard, the Mickey E-ticket and a new version of Toontown (C-ticket Fantasyland-style dark ride, unique flat ride, Mickey/Minnie M&G, kiddie coaster) could be the bridge between it and Sunset. I'm not too particular on what goes into Mermaid or Disney Junior.
Love the Muppets idea. Essentially a smaller variant of the Springfield expansions. However, I'd retheme Star Tours to Pigs in Space and make a new Muppet-centric film for the Muppet Theater (no more Waldo!).
The Indiana Jones mini-land could be great! An E-ticket boat ride and a family coaster themed to Temple of Doom would be a much better use of the space.
For Sunset, the B&TB replacement could be something like Music of Pixar, but featuring classic film songs/scores (Wizard of Oz, Singin' in the Rain, Mary Poppins, Casablanca, Breakfast at Tiffany's, West Side Story, My Fair Lady, The Sound of Music, Fantasia, Pinocchio, Snow White and the Seven Dwarfs, Swing Time/Top Hat). I'm pretty sure Disney has the theme park rights to all except Breakfast at Tiffany's and Sound of Music.
I'd also say a gangster dark ride could be a fun, less intense option for those not wanting to ride ToT or RnRC. I'd also change RnRC's soundtrack to be jazz/big band music so it could actually fit the 1930s/1940s vibe.
Of course, TDO wouldn't implement any of the ideas except maybe Mama Melrose's getting a Muppet theme and a Shanghai Pirates-style E-ticket themed to Indy.