Revised progression: The player starts with a red "Dash" ability. They gain a yellow "Glide" ability halfway through the Sunbaked Shallows (the tutorial area- yellow) and once they enter the Echoing Wilds (the crossroads area- blue) they gain a blue "Double Jump" ability. Only two of these Primary Color abilities can be equipped at once. You return the color to the Shallows after defeating the Sand Wisp (Shallows boss); when you first enter the Wilds, all paths except those to the center room are blocked off by grey water, and when you get to the center room, you return the color to the Wilds and all paths are unblocked. You can then enter any of the Secondary Areas. You can enter each Secondary Area only by equipping its respective color Abilities; for example, to enter the orange area, you must equip the dash (red) and glide (yellow) abilities. Once you reach the boss of the Area, these restrictions are lifted and you can use whatever abilities you like to defeat them. After beating a Secondary Area, you return color to it and gain a Secondary Ability. Only one of these abilities can be equipped at a time (in addition to your two Primaries), and they do not help you with color requirements to enter areas, but they are useful in boss fights and when fighting enemies. After beating all Secondary Areas, you can enter the Prism Tower and face Greyscale as laid out in my Story project.
P.S. Okay, apparently Indigo is a really important color (?!), so to avoid adding in ANOTHER area to design, we can just have it be in the lore that Huego fought his way through the old capital (Indigo City or whatever) to get to the Shallows. This isn't terribly impressive; the capital was abandoned anyway.