I'm still surprised that Capcom didn't announce RE7. I was 100% sure they will announce it on E3 but they didn't.
Feel free to add anything I missed.
Japanese third party published/Japanese developed games on PS4/XB1/WiiU at E3, per publisher:
Konami: Metal Gear Solid V: The Phantom Pain (PS4/XB1/360/PS3, actually globalized development between LA and bringing in 30% foreign staff, which given Konami, is surprising)
Square Enix: Final Fantasy Type-0 HD (PS4/XB1, PSP port)
Gung-Ho: Let It Die (F2P)
Bandai Namco: Dragon Ball XV (PS4/XB1/360/PS3), One Piece Unlimited World Red (Wii U, 3DS port)
Sega: Nope.
Koei-Tecmo: I think Nintendo is publishing Hyrule Warriors everywhere, but not 100% sure. However, they did show Dynasty Warriors I think?
Capcom: You can stream the PS3 version of Ultra Street Fighter IV on PS4 over PS Cloud.
Kemco: Alphadia Genesis (Wii U, Android game port)