One of the most notable changes is to how you play the game when a combo is starting. In Pokémon Battle Trozei, you would have a short time to move a Pokémon to continue the combo. However, in Pokémon Shuffle, once the combo is started, you have no control so the move is absolutely final and you have to be very careful with the move you choose.

In addition to this, you actually bring the Pokémon you use to create combos to attack the top Pokémon with your party rather than relying on set Pokémon. You can use four Pokémon at one time, but you can use items to remove one from the field of play to allow for easier capture.

You have a set amount of moves you can play in each stage requiring you to be more strategic in what you choose to do. Occasionally, enemies will create boxes that need links to be made adjacent to them in order to clear.

The stamina feature is the most noticeable change to the gameplay. Here, you get 5 hearts when you start the game and whenever you play a stage you will use a heart. These hearts are used in order to help control the duration of play. You can either wait 30 minutes to regenerate a heart or you can spend some jewels on purchasing multiple hearts to allow for you to continue. If you have zero hearts, you will be unable to play.

As of Version 1.2.0, it is now set so there are always 5 hearts to regenerate, even if you have purchased more hearts. You will use the 5 regenerating hearts first, before you go to the hearts that have been purchased by Jewels or gained through StreetPass.

Unlike the previous title in the series, you're no longer guaranteed capture when you finish a stage, Instead, it takes a page from the main series games and when the stage is complete, you throw a PokéBall by touching it on the touch screen. Each Pokémon has got a capture rate, which determines the chances of catching the Pokémon. If you have any turns remaining in the battle, this is added to it and makes the capture chances higher. The PokéBall will shake 3 times, each with a chance of the Pokémon coming out. If it's a success, you catch the Pokémon.

If it fails, however, you get the option of using a Great Ball. This doubles the chances of capturing the Pokémon, but costs 2500 coins to use.

From Version 1.2.0 onwards, a new capture feature comes in. Randomly, after a Pokémon has failed to be caught, you have a chance of getting a massive ~25% boost in the capture rate in addition to the increase added by the Great Ball. Using this, you can then pay the 2500 coins to use the Great Ball and have a higher chance of capturing the Pokémon. This chance is indicated by the Pokémon sweating and a light grey increase in the capture chance scale.

Mega Evolution is a feature that didn't exist in Pokémon Battle Trozei, despite the concept being around at time of its release. In this game, however, it is a major factor. If one of your Pokémon is capable of Mega Evolution, and it is the lead of your party then as you play through the stage, the special Mega Gauge will fill up. When it has filled up, it will cause your Pokémon to Mega Evolve, creating a lot of combos and more damage to the opponent.

Unlike Pokémon Battle Trozei, the Pokémon you use in the game are not simply standard Pokémon with set values. Instead, as you play through the game, you can level them up due to the experience earned by capturing a Pokémon in each stage. With each level up, the Pokémon will get higher Attack and will do more damage..

Enhancements were first spotted in Version 1.2.0 when a candy was seen next to all Mega Evolved Pokémon. From Version 1.2.2, you can start to get these enhancements through the Escalation Battles. These enhancements will boost your Pokémon, boot are limited to a one-time use, though the effect continues forever in the game.

The Mega Speed Up lowers the amount of matches needed to Mega Evolve

Escalation Battles are a special kind of battle introduced in Version 1.2.2 where as you complete a stage, it will level up and become more difficult with additional disruptions as you progress. To tie with this, the capture rate for the Pokémon goes up as the Level goes up and you get a variety of items, depending on the Pokémon you are facing.