Nintendo Japan has revealed 3 new Pokémon Nintendo 3DS themes: Pair Art Sets (ペアアートセット) and Pokémon Amie Substitute (ポケパルレのみがわり). The set themes cost 300yen while the Amie theme costs 200yen. All themes are available for purchase as of July 27th, 2016 on the Japanese Nintendo 3DS eShop store.

Pair Art Sets (ペアアートセット) - Latios and Latias / Sirknight and Ellade

Features: Features beautiful illustrations two Pokémon pairs. Set 1 features Latios and Latias while set two features Sirknight and Ellade.
Music: ORAS - Soaring Mirages (天翔ける幻) and ORAS - Mitsuru's Theme (ミツルのテーマ)

Pokémon Amie Substitute (ポケパルレのみがわり)

Features: The Pokémon Amie Substitute theme features artwork of the Substitute on the top and bottom screens.
Music: XY - Aiming Headings (ねらってヘッド)

Sources: https://www.nintendo.co.jp/3ds/theme/list/04075/index.html and https://www.nintendo.co.jp/3ds/theme/list/04076/index.html