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A significant update to Pokémon Shuffle for Nintendo 3DS was added to the eShop on March 23rd, 2016 bringing the games version up to 1.3.0. This large update add new elements to the game, new gifts for long time players as well as new features and items.

Update Check-in Bonus Gift

Those that Check-in from Wednesday March 23rd, 2016 until Tuesday May 17th, 2016 will receive 1 Raise Max Level (Max Level Up マックスレベルアップ) and 3000 coins. Players that haven't checked in for over 30 days will receive 10,000 coins and 30 Hearts.

Mission Cards

A new element to the game that was added in this update is Mission Cards (ミッションカード). Mission cards each have a specific task that needs to be completed with specifc requirements. Players can receive ★ according to the degree of difficulty of the mission. Once a certain number of ★ are collected via completing a cards objective, the player can receive a variety of rewards.

Only one Mission Card can be active at any time. When a Mission Cards objective is successfully completed, players are notified after the stage is finished.

① Mission Name
② Mission Objectives - Information on the task that needs to be accomplished to complete the mission.
③ Support Pokémon - To achieve the mission, players must use the listed Pokémon.
④ Gift Button - Reward list.
⑤ ★ - Lists the number of ★ a Mission Card will reward the player for completing.

Pokémon Maximum Level

Before the March 23rd, 2016 update, the maximum level any Pokémon could attain was Level 10. The Raise Max Level item can now be obtained to raise the ability for a Pokémon to increase by 1 level. Each Pokémon though has a set number of times that the item can be used though. For instance, Umbreon can only use the item 5 times. Players can see the current level of their Pokémon in the dex, how many items they've used on them and the remaining number of times they can use the upgrade item. In this update, only 24 Pokémon can level up.

· Bulbasaur (Grass type: Main Stage 2)
· Charmander (Fire type: Main Stage 4)
· Squirtle (Water type: Main Stage 3)
· Ivysaur (Grass type: Main Stage 59)
· Charmeleon (flame type: Main Stage 55)
· Wartortle (water type: Main Stage 57)
· Venusaur (grass type: Extra Stage 7)
· Charizard (flame type: Extra Stage 9)
· Blastoise (water type: Extra Stage 8)
· Sableye (Dark type: Sableye Main Stage 24, Mega Stone Main Stage 30)
· Altaria (Dragon type: Altaria Main Stage 118, Mega Stone Main Stage 75)
· Eevee (Normal type: Main Stage 5)
· Espeon (Esper type: Main Stage 71)
· Umbreon (Dark type: Main Stage 70)
· Sylveon (Fairy type: Main Stage 79)
· Lapras (Water type: Main Stage 43)
· Azumarill (Fairy type: Main Stage 76)
· Quilladin (Grass type: Main Stage 187)
· Braixen (Fire type: Main Stage 189)
· Frogadier (Water type: Main Stage 185)
· Druddigon (Dragon type: Event)
· Mew (Psychic type: Event)
· Kyogre (Water type: Event)
· Groudon (Ground type: Event)

New Items

Five additional battle and training items have been added in this update.

Exp. Booster S-M-L [けいけんちアップ（Ｓ・Ｍ・Ｌ）]: Increases a Pokémon's Exp. Points by +50, +200 or +1000.
Level Up (レベルアップ): Increases a Pokémon's Level by 1.
Raise Max Level (マックスレベルアップ): Allows a Pokémon to go above Level 10 by 1 level per item use.

Useful New Features

The UI has been updated to include a quick area jump icon located at the top of the stage selection screen. It also displays the number of S-ranked caught Pokémon for each zone. The number of caught Pokémon is now listed on the stage selection map as well. Recommendations for each stage have been added to the Nintendo 3DS version which were previously only in the Mobile version.

Amelia Recommendation Mark: A new Amelia Recommendation Mark which looks like a golden face of the tutorial girl Amelia has been added to various places throughout the game now including at the stage selection screen. When selecting supporting Pokémon, arrows have been added for super effective and not effective Pokémon.

Source: http://www.pokemon.co.jp/ex/poketoru/news/post.php/207/