In Japan, as many other things, airlines work differently from the rest of the world, LCC have not invaded the market just yet simply because ANA and JAL dominate the market.
In the past, they even agreed on sharing some airports, for example Yonago is ANA airport while Tottori is JAL airport only. At the beginning of the air travel, these airlines spotted nice locations in every destination and build their own hotels to accomodate the travellers at their destination. Hence, in Japan, you find still a lot of ANA hotels and Nikko, JAL Hotels. along the years, they have sold some of them but the domination remains. they also sell packages, have brochures etc. with the economic downturn, JAL suffered and went into administration for the last 10 years, however, they went out of danger this 2017 and started to expand again opening new routes etc.
Now LCC start expanding from Korea, Thailand etc. but ANA has also it own airline, you can now fly Peach or Vanilla when you are in Japan
Both airline, despite of their domination, still maintain a very good level of service and I typically fly ANA and love it.
Flying domestic is easy, you turn up at Haneda, 30mn before your flight and you are good, I never do this as I still have the European stress on long queues, strikes, etc but here, all is organised and smooth and flights are always on time (unless typhoon, snowstorm, real reasons…)
Flying international, if from Narita, takes more time since the airport is far away (90mn by bus, 1h15 by train) but equally well organised
I flew ANA in December on long haul and the service was impeccable, great food, they offer broth, what a great idea, they serve ice cream after the meal in economy, the cabin attendants go round during the whole flight offering tea, coffee, water, blankets, etc. I can only recommend them