So, today Nintendo shared the Top 25 for the first half of 2017 on the Nintendo eShop. Switch and 3DS only (RIP Wii U). Includes retail, download-only, and VC.
Nintendo 3DS - Nintendo eShop
01 - Monster Hunter XX (Capcom) [18.3.2017]
02 - Cube Creator DX (Arc System Works) [27.4.2017]
03 - Fire Emblem Echoes: Shadows of Valentia (Nintendo) [20.4.2017]
04 - Dragon Quest Monsters Joker 3 Professional (Square-Enix) [09.2.2017]
05 - Animal Crossing: New Leaf - Welcome amiibo (Nintendo) [23.11.2016]
06 - Terraria (Spike-Chunsoft) [21.4.2016]
07 - Super Mario Maker for Nintendo 3DS (Nintendo) [01.12.2016]
08 - Shin Megami Tensei IV Apocalypse (Atlus) [10.2.2016]
09 - Momotaro Dentetsu 2017: Tachiagare Nippon!! (Nintendo) [22.12.2016]
10 - RPG Maker Fes (Kadokawa) [24.11.2016]
11 - Mario Kart 7 (Nintendo) [01.11.2012]
12 - The Legend of Zelda: Ocarina of Time 3D (Nintendo) [01.11.2012]
13 - Miitopia (Nintendo) [08.12.2016]
14 - Fire Emblem Awakening (Nintendo) [30.1.2013]
15 - Yo-kai Watch 3 Sukiyaki (Level-5) [15.12.2016]
16 - Pokémon Sun (The Pokémon Company) [18.11.2016]
17 - Pokémon Moon (The Pokémon Company) [18.11.2016]
18 - Poochy & Yoshi's Woolly World (Nintendo) [19.1.2017]
19 - Tomodachi Life (Nintendo) [18.4.2013]
20 - Pro Yakyuu Famista Climax (Bandai-Namco) [20.4.2017]
21 - Super Smash Bros. for Nintendo 3DS (Nintendo) [13.9.2014]
22 - Dragon Ball Heroes: Ultimate Mission X (Bandai-Namco) [27.4.2017]
23 - Monster Hunter Generations (Capcom) [28.11.2015]
24 - The Alliance Alive (FuRyu) [22.6.2017]
25 - Story of Seasons: Trio of Towns (Marvelous) [23.6.2016]
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https://www.nintendo.co.jp/software/feature/3ds-ranking.html
Nintendo Switch - Nintendo eShop
01 - Snipperclips: Cut it out, together! (Nintendo) [03.3.2017]
02 - Minecraft: Nintendo Switch Edition (Mojang) [12.5.2017]
03 - Mario Kart 8 Deluxe (Nintendo) [28.4.2017]
04 - Kamiko (Flyhigh Works) [13.4.2017]
05 - The Legend of Zelda: Breath of the Wild (Nintendo) [03.3.2017]
06 - ACA NeoGeo Metal Slug 3 (Hamster) [03.3.2017]
07 - ARMS (Nintendo) [16.6.2017]
08 - 1-2-Switch (Nintendo) [03.3.2017]
09 - ACA NeoGeo The King of Fighters '98 (Hamster) [03.3.2017]
10 - Othello (Arc System Works) [03.3.2017]
11 - VOEZ (Flyhigh Works) [03.3.2017]
12 - Super Bomberman R (Konami) [03.3.2017]
13 - New Frontier Days: Founding Pioneers (Arc System Works) [03.3.2017]
14 - Blaster Master Zero (Inti Creates) [03.3.2017]
15 - ACA NeoGeo Metal Slug (Hamster) [30.3.2017]
16 - Human Resource Machine (Flyhigh Works) [08.6.2017]
17 - Flip Wars (Over Fence) [18.5.2017]
18 - Shovel Knight (Yacht Club Games) [30.5.2017]
19 - Ultra Street Fighter II: The Final Challengers (Capcom) [26.5.2017]
20 - Unholy Heights (Mebius) [13.4.2017]
21 - Wonder boy: The Dragon's Trap (DotEmu) [18.4.2017]
22 - Seiken Densetsu Collection (Square-Enix) [01.6.2017]
23 - Puyo Puyo Tetris (SEGA) [03.3.2017]
24 - Mighty Gunvolt Burst (Inti Creates) [15.6.2017]
25 - Thumper (Drool) [18.5.2017]
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https://www.nintendo.co.jp/software/feature/switch-ranking.html