Epcot seemed to do a good job at this when it was built. Paths are wider, attractions were built to eat up more guests (i.e. Horizons), the park was larger to distribute crowds better, and an overall master plan of the layout made it easy to navigate.
Magic Kingdom needs higher capacity attractions, wider walkways, efficiency corridors that are used to specifically speed up traffic flow during peak periods, and a re-evaluation of the parks master plan and flow to help de-clutter high traffic areas.
Here is a my initial thoughts by land...
MAGIC KINGDOM ENTRANCE
-Continue walkway from entrance to Grand Floridian to ease pressure off of transportation for those wishing to walk to the Grand Floridian or Polynesian Resorts.
-Reconfigure bottleneck at bag check.
-Ideally expand the width of the entry tunnels to Main Street USA
MAIN STREET USA/THE HUB
-Feature more character meet & greets in the Town Square Theater (especially after the Princesses move to their Fairytale Hall) an less in the Town Square.
-Create a more permanent Main Street bypass along the backside of Main Street East shops. The bypass would be themed better than a parking lot, but would help with traffic flow and parade viewing capacity during peak periods.
-Along the Main Street West emporium shops, create a smaller efficiency corridor/arcade similar to the arcade on Buena Vista Street at DCA with little to no merchandise clutter that serves as a main corridor to traffic to pass through during peak periods and bad weather.
-Expand the seating for Casey's Corner/Ice Cream Parlor area.
-Expand the walkways near First Aid and Crystal Palace.
-Create designated stroller parking area near Crystal Palace.
-Create a better queue area for PhotoPass set ups near the Rose Garden entrance/MickeyMinnie topiary.
-Expand the pathway in the Rose Garden to be used a efficiency corridor during peak periods.
TOMORROWLAND
-Move Toy Story Green Aliens merchandise cart closer towards Carousel of Progress and Buzz Lightyear Exit to clear a bottleneck area.
-Reconfigure & Re-purpose the Tomorrowland Terrace restaurant to serve as another DAILY operating eating establishment and also serve a primary efficiency corridor that connects to the Main Street East permanent bypass for peak periods, parades, and fireworks.
-Replace the Tomorrowland Speedway with a new high capacity Tomorrowland attraction.
-Build another eticket Tomorrowland behind Buzz Lightyear/Carousel of Progress.
-Update Carousel of Progress to draw in more crowds.
-Replace Stitch's Great Escape with new attraction to draw in more crowds.
-Rebuild Space Mountain's track to allow for higher capacity trains, on-board audio, more effects, separate wheelchair loading platform like Disneyland's, all while still maintaining it's classic layout and thrills. Also reconfigure/remove stairs in stand-by line to make stand-by line wheelchair accessible reducing impact on Fastpass line.
-Expand Cosmic Ray's Starlight Cafe to allow more capacity. Create easier way to monitor traffic flow in and out of the building during peak periods.
-Replace the current Astro Orbiter with a high capacity model.
-Utilize the Tomorrowland Stage for more events even if that means more Club 626 Dance Parties.
-Move the Water/Granite Sphere to a different location toward the open area near Space Mountain.
-Utilize the area between the Space Mountain restrooms and the attraction for something.
-Add Sorcerers of the Magic Kingdom portals to Tomorrowland.
-Expand photo viewing area at Buzz Lightyear Exit for better traffic flow possibly allowing for an indoor Buzz Lighyear meet and greet as well.
FANTASYLAND
-Expand the queue area for the Fantasyland Train station
-Create a designated stroller parking area north of the carousel in the castle courtyard.
-Refurbish Peter Pan's Flight to increase capacity, refurbish an aging classic, add new effects, and reconfigure the queue to make it more enjoyable like Winnie the Pooh's.
-Relocate some Sorcerers of the Magic Kingdom portals to be spread throughout the land better to reduce crowds behind the castle.
-Possibly Relocate the Bibbity Boppity Boutique to outside of the castle in an existing store and move that store into the castle.
-Redo the medieval fair facades in the castle courtyard to match more like Disneyland's Fantasyland.
LIBERTY SQUARE
-Expand the walkway along the riverfront across from the Liberty Tree Tavern to serve as an efficiency corridor during parades and peak times.
-Create a better designated stroller parking area on the sides of Columbia Harbor House/Hall of Presidents.
-Redo the Haunted Mansion queue to utilize space better, redo the interactive queue to match more with the inside, and spread the interactive queue out.
-Expand the restrooms in the Liberty Tree Tavern
-Utilize the Diamond Horseshoe more.
FRONTIERLAND
-Expand the boardwalk along the riverfront to serve as an efficiency corridor during parades and peak times.
-Update Country Bear Jamboree to reflect more modern country music to draw in more crowds. Reconfigure Country Bears exit.
-Create better traffic flow in and out of Peco's Bill's during peak periods.
-Create a better designated stroller parking area near or across the street from Country Bear Jamboree.
-Expand walkways near the Splash Mountain/Big Thunder Mountain bottleneck areas including under the Frontierland Train Station.
-Reconfigure entrance/exit of the Frontierland Train Station for guests traveling in wheelchairs.
-Reconfigure queue to allow wheelchairs to access either the standby or Fastpass queues without entering from the attraction exit.
-Utilize the Aunt Poly's area of Tom Sawyer Island as a small outdoor food vending location during peak hours offering unique treats to encourage guests to visit an underutilized attraction.
-Create a designated meet and great for Woody, Jessie, and Bullseye.
ADVENTURELAND
-Create a better exit corridor through the gift shop at Pirates that still encourages guests to browse, but also reduces traffic jams.
-Reconfigure entrance to the Pirates League.
-Utilize Tortuga Tavern more often with more unique Adventureland food menu.
-Move Pineapple Dole Whips to the Sunshine Tree Terrace for more register capacity and more queue room.
-Remove the Swiss Family Treehouse, move Aladdin's carpets to this new area with a new Agrahbah themed additions and meet & greet. (This also reduced bottleneck in Adventureland and restore the Tiki Room plaza area. Possibly add a new attraction: eticket or high capacity dark ride
-Expand and create a better designated stroller parking area in the center of Adventureland. (not along the walkway towards Pirates)
-Redo the Tiki Room to include Lilo & Stitch (after removing Stitch from from Tomorrowland) to breathe new life into the attraction and give 626 a home.
-Redo the old Adventureland Veranda area into a better storage/cast member area it's already being utilized as as well as better Adventureland meet and greet for not only the Fairies but other Adventureland characters. Move Dole Whips to the Sunshine Tree Terrace.
-Move the Smoking Location to a better spot not as close the main walkway.
-Expand the path near the (now former) Swiss Family Treehouse.
-Expand the breezeway between Liberty Square and Adventureland near the restrooms.
OVERALL PARK
-Create desginated main thoroughfares/corridors through all major gift shops for ease of access, traffic flow, and merchandise restocking.
-Emporium should contain the largest selection of specific and generic park merchandise. Each land should contain a flagship store that contain land specific and generic park merchandise. Smaller land stores and stores found at attraction exits should contain ride specific and land specific merchandise only with limited generic park merchandise.
-Each land should contain a primary walkway used as an efficiency corridor that has limited clutter. Land containing the parade route should always have a parade bypass walkway for traffic flow purposes.
-Each land should contain at least one major designated and specifically designed stroller parking area. All areas allowing stroller and ECV parking will be labeled.
-During peak periods requiring crowd control, map inserts will be included to help aid guests in how traffic patterns are being controlled to ensure guests understand the method behind the madness.
I think these ideas will help unclog the Magic Kingdom using a realistic approach that will ensure the park can handle average crowds better and ensure the park maintain good traffic flow during peak periods. Also to answer your question, yes, Fastpass will still be available at this park. It would exist at it's current locations, but would not include the upcoming additions for Fastpass+.