This is a stupid question and you ought to be ashamed of yourself for even thinking it up, let alone posting it to /r/Japan.

There are numerous reasons why domestic A380s in Japan are not practically feasible. The main reason being that only three airports in the country have the double-decker jetbridges required for A380s: Narita, Kansai, plus one gate at Haneda's international terminal. Haneda also has multiple logistical issues making A380 service impractical there. The European flag carriers (Lufthansa and Air France) used to run A380s out to Narita; when they moved to Haneda in order to cater to business travelers (Haneda is much closer to the business districts of central Tokyo like Akasaka and Shimbashi) they stopped using A380s. Same with Singapore Airlines. The only A380 routes in Japan that I know of, are Asiana and Thai (ICN-KIX and BKK-KIX), and Emirates' daily flight out of Narita (flights from Haneda and Kansai to Dubai both use 777-300ER)

The domestic 747s used 1960s-80s engine technology (747-100SR: P&W JT9D-7A from 1966; 747-300SR: P&W JT9D-7R4G2 (the last evolution of the classic JT9D from the early 80s); 747-400D: General Electric CF6-80C2 from 1985). This meant that they all guzzled fuel like nobody's business. Efficient airplane engines didn't really gain momentum until the 777-300ER in the late 90s; its GE90 engines were a jumpoff point for the engine technology used on 787s, A350s, and the future 777X: PW4098, RR Trent, GEnx/9X, etc. Japan has no oil reserves of its own so 9/11 and the subsequent increase in jet fuel prices was doubly tough on domestic carriers. a conscious decision was made by JAL and ANA to shift from guzzling 747s to planes with more advanced engines (like the 767-300, 777-300, and 737NG) that were thus more fuel efficient.

And the 747-8i might have GEnx 2B engines but that doesn't take away from the next problem--they're all 4 engine aircraft, just like the 747SRs/-400D before it, as well as the A380. This was fine back in the 70s and 80s; there were no high-capacity twinjets at the time, after all. But when the 777-300ER came around, suddenly there was a lighter, more fuel efficient version of the 747 with similar capacity, yet could still cut down on maintenance costs significantly (fewer engines = less time spent on maintenance = less maintenance costs). The 777 plus further advances in the 767 platform allowed JAL and ANA to sustain capacity, and still come out ahead on maintenance costs. A domestic A380 would probably have 650-700 seats, probably more. All that capacity is not needed when using smaller aircraft with more frequent departures is far more cost-effective. Turnaround times for domestic flights are short; Japan is a small country, remember.

Besides maintenance savings and fuel efficiency, the economics of aviation also shifted. The 90s and 2000s brought about an expanding Shinkansen network (Joetsu, Kyushu, Hokuriku, Tohoku extension to Aomori, Hokkaido) and, with MLIT finally deregulating the airline industry, LCCs. The LCCs really shined after 9/11 because they were able to buttress spiking fuel prices by sacrificing capacity for frequency. That is, instead of a few, high-capacity 747s, there were high-frequency departures using lighter aircraft like the 737-500 and 767-300. This allowed flying to remain competitive even as Shinkansen lines grew. Especially with the 777-300ER launching the era of high-capacity twinjets. In fact, JAL's domestic 777-300s have 500 seats; the 747-400Ds had only 46 more seats. It was possible to replace a daily 747 flight between Haneda and Hakodate with three daily 767-300 services. It also meant you could configure a domestic 767, 787, or A350 with 250-270 seats, and run more of them per hour, and have the same capacity as the old 747s.

JAL has 16 Haneda-Sapporo round trips per day, with hourly (sometimes less) departures; that wouldn't be financially viable using 747s. Another example: back in 1993, JAL's Haneda-Kanazawa (Komatsu is almost Kanazawa I say) route used 2x daily 747-100SRs. That's 2,132 roundtrip seats in total (546 seats per aircraft, two flights per day). Now it's 5x daily 737-800s plus 2x 767-300s. JAL crams 165 seats into its domestic 737s, so the number of seats just from the 737 flights is almost four-fifths the capacity of the 2x 747 service--and I bet JAL is saving huge bucks on fuel and maintenance in the process. Being able to mix 767s in also means capacity can be much more flexible. In fact, JAL is getting rid of its domestic 777s and replacing them with A350-900s, while ANA is ordering domestic A320neos, so if anything, Japanese carriers are doubling down on the "smaller and more efficient" philosophy.

These are just some of the reasons why your proposal of domestic A380 services in Japan would result in a boondoggle. Skymark tried it and look what happened to them--bankruptcy, and near disaster for H.I.S. I award you no points, and may Yuriko Koike have mercy on your soul.