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As with any other game, Super Mario Bros. Online has went through many changes throughout its developmental cycle. Since the creators had to attend to real life matters, many ideas and areas were not able to be fully implemented, or implemented at all, into the game.
Alpha Super Mario Bros. Online

A picture of the alpha version of the game. Notice the different HP, FP, and Experience Point bars.

Areas

Super Mario Bros. Online was supposed to feature many more areas on top of the currently released ones. No work was done on these areas, but there were some ideas for them.

Volcano
A volcano area was planned to be in the game. It is unknown where it was supposed to be placed or when it would have been put into the game.

Cave(s)
The game was supposed to feature small caves inside mountains that would play the song of when you went through a Warp Pipe in Super Mario Land, and a large cave area was supposed to be placed to the left of Kinopio Village. This large cave would have led to another desert, but the entire cave was scrapped because the creators realized how little time they had left and instead worked on Flower Hills.

Additionally, there were going to be Drill spots that would lead to underground caves, but that idea was thought of just before development stopped.

There now exists miscellaneous caves around areas in the Mushroom Kingdom carrying minor item bonuses such as coins. There is a large expansive cave area separate from the desert area called Shy Guy Caves, which bridges the gap between the BeanBean Kingdom and Mushroom Kingdom. 

Underneath Dry Bones Desert
Dry Bones Desert currently features a very large red pipe on one of its screens. The player would be able to fall into this pipe from a cloud area and explore a large cave underneath Dry Bones Desert.

Larger Peach's Castle
Peach's Castle was originally going to be much larger than it is right now, but one of the creators, Kimimaru, was running out of time to release a very large update and bring the game out into its final form. It is unknown what this larger version of Peach's Castle would have featured.

Joke's End
Interestingly enough, this is actually the tutorial area, and it resides in the Beanbean Kingdom (hence the "?" for the kingdom location). This would be one of the later areas of the Beanbean Kingdom, and the player would even be able to see a glimpse of the tutorial section as he or she progressed.

Unnamed Swamp Area
A swamp area was conceived of, but never considered being put into the game.

Unnamed Cloud Area
This area would have been the second-to-last area of the game, but which kingdom it would have been in is unknown. It would be accessed using the High Jump Special Badge.

Bowser's Castle
This would have been the last area of the game, with the boss being Bowser himself. No other information is known about it except that it would have been extremely difficult.

Pit of 100 Trials
This area would have featured 100 consecutive floors that the player must go through. The player would not be able to rest after each floor, and if the player died on any given floor the player would have to start back from the 1st floor. On the 100th floor would be a boss that would drop a special item. It is not known where this would have been placed.

Items

Fire Protection
FireProtection

This Special Badge was intended to be dropped by Bob-Ombs and would allow players to walk through walls of fire that prevented them from getting to the Volcano area. However, before development stopped, it was decided that it would be obtained in the Volcano. Unfortunately, neither the Volcano area nor Fire Protection made it into the game.

Item Description: A neat badge that allows you to walk through fire (Special Badge).

High Jump
This Special Badge was conceived of very early in the game's development. It was supposed to be the third Special Badge that granted an ability. By standing under a High Jump spot and pressing the Action Button, players would be able to jump to small cloud areas and fall down from them to land in spots otherwise inaccessible. This idea would also have been used to access the second-to-last area of the game, an unnamed cloud area.

Unfortunately, the developers delayed implementing the High Jump badge and instead made the Drill badge. As development time neared its end, they realized that it would be impossible to include the High Jump badge into the game.
HighJumpSpot

Although no item exists for the badge, there is a High Jump spot. The badge was supposed to be colored red and correspond with the colors of the Spin Badge.

Experience Point Plus Plus
This Special Badge was going to be put in the Mushroom Kingdom Arcade and would be obtained if the player got a specific score in one of the minigames. It was supposed to give double the experience of the Experience Point Plus badge. However, it was dismissed because the developers felt it would take away the uniqueness of the original Experience Point Plus badge.

Minigames

Two Player Whack-A-Monty
The Mushroom Kingdom Arcade was originally going to feature many more minigames other than just Dodgebill. One of the games was a two player version of Whack-A-Monty. This version would have Green and Gold Monty Moles; the former would give the players more time, and the latter would give the players three points each. Unfortunately, the idea was scrapped before the Mushroom Kingdom was even made.

Unnamed Target Shooting Game
This was the first single-player minigame planned for Super Mario Bros. Online and was conceived by hydrakiller4000. hydrakiller4000 was unable to find a place for it early on, so it was going to be added to the Mushroom Kingdom Arcade.

Players would pick up balls that looked similar to Waluigi's Slingshot Balls and throw them at moving targets to score points. Unfortunately, since development time was nearing its end, this minigame had to be cut from Super Mario Bros. Online.

NPCs

Password-Changing NPC
This was, without a doubt, one of the first NPCs ever created in Super Mario Bros. Online. When talked to, this NPC would ask the player for his or her current password. If the entered password was correct, the NPC would then ask the player to enter a new password that would be used for login. Sadly, as development went on, this NPC was completely forgotten, and the creators never put it in the game.

EDIT: This NPC has been put into the game and is now in Mushroom Town.

Favors

Peach's Letter
This favor was originally going to be fairly short and not include the Goomba on Mushroom Kingdom Path, who was going to be used for a separate favor. However, the developers wanted to make a longer, more challenging favor and decided that it was best to combine the two favors into one.

Drillbit Crab Shell Favor
Originally, this favor required 5 Drillbit Shells, yielding a reward of 3 Melons, as opposed to 3 shells for 5 Melons.

Battle System

Action Commands
Each attack would have had an action command that can be performed to increase the damage it takes in turn-based battles, similar to the Mario RPGs. There would have also been defensive action commands to reduce the damage enemies deal to the player.

Character Special Attacks
Each character was going to have his/her own special power that can be used in turn-based battles. To use these powers, players would first have to successfully execute action commands to fill up the Power Meter. These powers would have had ranks and would have been upgraded at certain level intervals. The ranks are as follows:

Mushroom Rank
Flower Rank
Star Rank

SMBO Empty Mushroom Power Bar

Empty Mushroom Power Bar

SMBO Mushroom Power Bar

Full Mushroom Power Bar

SMBO Flower Power Bar

Full Flower Power Bar

SMBO Empty Flower Power Bar

Empty Flower Power Bar

SMBO Star Power Bar

Full Star Power Bar

SMBO Empty Star Power Bar

Empty Star Power Bar

Unfortunately, due to time constraints and uncertainty of how exactly to implement these features, they were never put into the game.

Trivia

- On November 27, 2011 a post was made on the official forums by Kimimaru stating that the game is back in development, so there is still a possibility that some of these beta elements can be implemented into the game.

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