They did have some new announcements but people were disappointed because the E3 didn't live up to (some ridiculous) expectations.
Some things announced:
-Animal Crossing: amiibo festival - a (free?) boardgame Animal Crossing spinoff for Wii U
-Metroid Prime Hunters Federation Force - a spinoff Metroid multiplayer game for 3DS
-Hyrule Warriors 3DS - a port of the game to 3DS including new characters
-Zelda Triforce Heroes - a multiplayer co-op online or local 3DS game that looks like A Link Between Worlds
-A Mario and Luigi / Paper Mario crossover game for 3DS
-Animal Crossing amiibo line
-Yokai Watch
Also, revealed during E3 time but not the digital presentation:
-Pokemon Super Mystery Dungeon
-Chibi Robo Zip-Lash and amiibo
-Bravely Second
-some other smaller games I can't quite remember
As well as more info on Happy Home Designer, Star Fox (actual game footage) and Mario Maker.
People were upset because:
-No full Animal Crossing Wii U game
-No full Metroid game
-No full Paper Mario Wii U game
-other games they wanted