I used to think that the level design of Super Metroid was so complex with its connected world, alternate paths, folded level design, and high level sequence breaking design, that it would be impossible to understand how Nintendo did it let alone teach others how to design similar quality levels. I thought that about a year ago. Since then, writing for the Critical-Gaming Blog has developed my critical eye to break down Super Metroid's design.

Here's how they possibly did it, and how you can too.

• Include little to no artificial restrictions. If the main or intended order of progression involves getting a sword, then shield, then horse, don't prevent the player from using the horse if they manage to obtain it before getting their shield and/or sword. If the player gets it, then make sure they can use it. If the player figures out how to solve the mystery, don't make them talk to the fixed order of NPCs before being able to input the right answer. Creating restrictions like these are a type of invisible wall that players will run into.
• In Super Metroid, if the player finds a powerup, weapon, or special item, they can immediately use it. For example, in the video, the player obtains hidden super missiles (7:30) far earlier than he would have on the main path and uses them to dispose of Kraid easily (11:00).

• Create "locks" on progression that are unlocked with the use of character abilities as "keys." When the player can obtains a new abilities that upgrade how they explore the game world, it becomes easy to design paths that are restricted until the player uses that ability. In this way a "lock" can be created without necessarily making a physical barrier. This design is great because of how the existing stage is transformed by the new abilities giving the player new areas to explore and new ways to move around previously visited areas. If the ability isn't an exploration enhancement (ie. a weapon) creating specific "locks" is the next best thing.
• In Super Metroid, obtaining the morph ball powerup, the speed booster, gravity suit, space jump, and grappling beam obviously help Samus get around the environment in new ways. Additionally, there are barriers, doors, and areas that can only be opened by using missiles, super missiles, bombs, power bombs, the screw attack, the ice beam, and the wave beam. In this way, the Super Metroid weapon powerups are designed to transform the world in addition to augmenting Samus' firepower.
• The combination of exploration enhancing upgrades and "ability locks" is used to restrict and guide the player along the main paths of progression. At the same time, this design ensures that by obtaining a single powerup out of order/early, the potential paths of progression dynamically shift and open up.

• Design the overall level with as many folds (normal, accordion, origami) as possible and maximize space. By using folds to maximize space, zones are naturally created. These zones are very useful to have when you start adding in alternate paths. Even when separate rooms or hallways are disconnected from each other, their proximity will create opportunity to create bridges and connections between them. If you want the player to be able to grasp the bigger picture, it helps when the bigger picture makes sense spatially. Also, the player can save time and break sequences by avoiding the need to travel back through an area after the crease especially if they've obtained an early ability.
• In Super Metroid, the overall game map is packed (see above). Aside from the many connections individual rooms (cells) have to their neighbors, the entire top half of the game map is connected to the middle via 4 elevator shafts. Because everything is so compactly designed, the player is never too far from a main or alternate path to the area they want to be.

• The main path must be designed around the simple use of the game's core mechanics while providing alternate paths designed around advanced mechanics/techniques. A new player must feel guided through the game by how the level restricts access to areas until the player is ready to traverse them. This is how most games are designed. To limit the new player to the main path, the barriers don't don't have to be so obvious with the excessive use of locked doors for example. Instead, if you design an alternative path that's inaccessible unless the player uses an advanced technique, then everyone wins.
• In Super Metroid, the entire game is designed so that the player can slowly but steadily make it from the beginning to the end. However, Samus features some hidden abilities/mechanics that give players the power to access many new paths if they have the skill. The WALLKICK is a key secret mechanic. I played through the entire game before realizing I had the ability to scale walls all along. As you can see in the video, the player uses this advanced technique to access many powerups and areas far earlier than the main path player would.

• Include useful/functional secrets like alternate paths and powerups. It's nice to find or collect secrets in a video game. It's even better to find/collect secrets that have real impact on the gameplay or the player's progression through the game. Some examples of substantial secrets are powerups that give the player unique abilities (Tanooki Suit), or hidden paths that connect one part of a game world to another (warp whistle). The interesting part of a secret is, players tend to remember/collect them over time. Nowadays, gamers who grew up on Super Mario Brothers or SMB3 have a little database of secrets for every level. For one reason or another, secrets just stick with us.
• In Super Metroid, the many hidden missiles, super missiles, power bombs, energy tanks, and reserve tanks upgrades can be uncovered at any time as long as the player can get to them. It's clear in the video that the player knows where all the powerups are can gather powerful abilities early in the game. For the player who doesn't have everything mapped out, simply remembering where secrets are helps the player reclaim powerups mostly likely earlier than when they first stumbled across the secret on previously play throughs. 

• Balance mandatory and optional events like bosses. It's neat that players can rearrange their progression through a game to achieve super low times. As a designer, we want the player to find their own way to play through the core experience, not skip everything they can. In order to ensure that even the sequence breaking speed runner plays the game/level you design, you must balance the number and the type of mandatory events/obstacles the player must go through to complete the game.
• In Super Metroid, there are at least two mini bosses (Spore Spawn (green), Crocomire (red) see above) that the player doesn't have to fight at all. At the same time, the final elevator to access the final area and go fight Mother Brain can only be unlocked after defeating the the 4 major bosses (Kraid, Phantoon, Draygon, Ridley).

LBP and Beyond

LittleBigPlanet is a great game for designing sequence breakable levels for many reasons.

1. The creator gives players a nice large area to work with.
2. Players have full control of a variety of switches.
3. Because everything is physics based, all the puzzles, obstacles, and elements easily yeild highly organic design. 
4. There's a high level of potential emergence in the core design for creating advanced paths, secrets, and powerups.

I am currently working on a LBP level that demonstrates everything we've covered about level design so far. Should be very interesting. Stay tuned.