Indiana Jones would come to the park, just not in a ride. Instead, young Indy would star in the Young Indiana Jones Adventure Spectacular. Located at the Festival of Fools arena, the entire show would have been performed inside a circus tent with - get this! - the Disneyland Railroad actually running through the tent! Remember the locomotive chase from the beginning of Indiana Jones and the Last Crusade? Disney planned to perform exactly that right inside the tent ... unfortunately, Operations said it would interfere with the Disneyland Railroad passengers too much.
The Muppets would have begun their in-park presense (Disney was expecting to buy them at the time, although Jim Henson's death would delay the purchase by a decade) in Here Come the Muppets, a clone of the show at Disney-MGM Studios which would have been performed in the Videopolis theater.
Only one announced attraction - the Dick Tracy Musical Revue: Diamond Double Cross - would get the greenlight.
The Muppets would continue their park invasion with Kermit the Frog Presents Muppet Vision 3D (note that it's not Jim Henson Presents at this time). Unbelievably, this clone of the Disney-MGM Studios attraction was considered to have been located in the Main Street Opera House, replacing Great Moments With Mr Lincoln. Barring that, the attraction was also planned to have been located in a new land:
Mickey's 65th Birthday would have been celebrated in a year long celebration, including the opening of Mickey's Starland - which we all know as Mickey's Toontown. As well as possibly holding Muppet Vision 3D in its downtown area, Mickey's Starland would additionally have included The Little Mermaid, a clone of the dark ride planned for Disneyland Paris.
The next year would have seen the opening of the legendary Tomorrowland 2055 (named after the 1955 opening date of Disneyland. Overseen by George Lucas, the land would have included Alien Encounter - the same attraction that would open at Walt Disney World, and The Timekeeper, a clone of 'De Temps en Temps' from Disneyland Paris.
Brand new would be Plectu's Fantastic Intergalactic Revue, located in the Carousel of Progress theater, with Battle Droids upstairs.
Dick Tracy's Crimestoppers, a high-speed car chase attraction, would combine "state of the art technology with a classic story from the past".
1999 would expand the Crimestoppers locale into a whole new land - Hollywoodland, headlined with a clone of Disney-MGM Studios' The Great Movie Ride.
Roger Rabbit's Toontown would have been present with the Toontown Trolley simulator attraction and Baby Herman's Runaway Baby Buggy ride, a wild dark ride that probably evolved into Roger Rabbit's Car-Toon Spin. Superstar Television, a green-screen show, would have completed the land.
To conclude this post, here's a video segment featuring some of the mentioned attractions taken from 'The Disneyland Story: 35 Years of Magic':