There are a few reasons why the Super Hornet is a good choice.
Firstly it’s operational today. Depending on the reasons/urgency deals can be struck, Australia got the SH very quickly to fill a pressing need.
It used by the USN which operates F18’s, allowing shared stores, maintenance, parts, training etc. benefiting the US and Japan and local allies. The USN intends to use the F-18 even after the F-35 comes on line and as such it has a long life expectancy.
It has modern avionics and technology and it can be upgraded to fill the EW role if required. It is fairly unique in this role. Wiring can be fitted to any and all builds allowing conversion at a later date.
It is carrier capable. It could also be conceivable that Japanese F-18s could be decked or operate from a US, UK or French carrier. Allowing greater training and operational opportunities. Australia also operates this aircraft allowing easy basing of Australian aircraft to Japan or Japanese aircraft to Australia.
It is a 2 seater allowing options and capabilities that entails which may become important on several mission types.
It is twin engine, reliable, well supported and offers capabilities that EF and even the F-35(A) won’t offer conceivably at all (2 seats, immediate us carrier capability and specific EW variants).
Japan has not been afraid of operating more than 1 type of aircraft. So after purchasing the F-18 SH it may be able to acquire F-35/F-15/EF at a later date (or both/all) or choose to develop its own aircraft.
Australia has proven that it is possible to quickly build and adopt the F-18 SH to fill a capability gap. She may not be pretty, nor the fastest, nor the most agile. But is a proven and capable aircraft that fits into many situations.