Skyscanner won't give you the budget airlines like AirAsia X, Jetstar, Peach, Spring Airlines etc. Also missing China Airlines and probably few others.
Aircalin, Air Do, Shenzhen Airlines, Juneyao Airlines, ZIPAIR, Skymark Airlines, Solaseed Air, Starflyer, Vanilla Air, Royal Brunei Airlines, Hong Kong Airlines, S7, Aurora, Air Tahiti Nui, Lion Air, Cebu Pacific, T'Way Air, and NokScoot also fly into Tokyo.