Out of those, I'd say the ranking for Japanese language learning + pastoral care would be as follows:
1. Sophia / Doshisha / Seikei (if your university offers it) <-- These are truly and utterly the best for improving your Japanese and for taking care of you while abroad.
2. Hokkaido (exceptional location of Sapporo albeit excruciatingly long winter)
3. Yokohama / Waseda / Keio. <-- Waseda and Keio are pretty average for Japanese teaching and their pastoral care can be OK. Waseda's location is great but Keio's is pretty bad... On the upside, both have amazing reputations in Japan (much like Sophia). Yokohama has pretty decent location and everyone I know who's gone here has had a pretty awesome time. Yokohama's also considered very prestigious.
4. Nagoya, Osaka, Meiji, Tokyo <-- Have absolutely no idea about these. I have Japanese friends who have gone here but don't know any exchange students. Your experience as an exchange student will be completely different to that of a Japanese student's, so that's why I can't comment too much. What I can say, however, is that they're not particularly well known for their established exchange programmes, so it's probably a safe bet to say they're average or below.
Complete last. Kyoto University. <-- Never, ever go here.
When you go on your year abroad, whatever you do, do not choose Kyoto University. It has one of the absolute worst exchange programmes and you'll find that your level of Japanese actually gets worse.
For exchange, the best are Seikei University > Sophia University = Doshisha University > International Christian University = Kwansei Gakuin University > Waseda University = Kyushu University = Hokkaido University = Keio University = Yokohama National University = Ritsumeikan University > all others.
I have no idea about Tokyo University, admittedly. Kyoto University is the absolute worst. 100% would not recommend.
The problem is that even though certain Japanese universities might have an excellent reputation in Japan, their exchange programme could be very bad. In other words, although Kyoto University is considered the second best, if not the best, university in all of Japan, it has one of the absolute worst exchange programmes. It's so bad that Edinburgh doesn't allow its students to do exchange there unless they're already fluent in the language. So many bright Edinburgh students were going to Kyoto and coming back worse than when they went.
Kyoto, for some bizarre reason, forces its students to take GCSE-level courses in English...
To add more detail I can say that Seikei is the best of the best due to its exceptional accommodation and intensive one-on-one courses. You'll literally be studying intensive Japanese with a tutor all to yourself every single day. Needless to say, all those that go to Seikei come back extremely, extremely competent in Japanese. That said, first con is that the university itself is super east of Tokyo and would take 30+ mins by train to get to central locations like Shinjuku and Shibuya (unlike Sophia which is in the heart of the city). Second con is that Seikei's domestic rankings are sub-par.
Second would be either Sophia or Doshisha. Both have exceptional pastoral care (Sophia offers one-on-one mental health counselling every single week if need be), exceptional language courses and equally exceptional locations. Both also have some of the best domestic rankings. For some people, a con would be that unlike Seikei (which barely has any exchange students), both have many international students. Not thaaat much though and it definitely doesn't take away from the 'authentic' Japanese university experience (I speak from experience). Many small universities with low numbers of international students heavily struggle with extremely important things like pastoral care which both Sophia and Doshisha excel at.
Moving on, I've heard good things about Kyushu but only know 1 person who went there. Hokkaido is a great university with an excellent location in central Sapporo; but, the drawback is that although the university is famous, its exchange programme is OK / average and Hokkaido has a very, very long winter. Waseda's exchange programme is OK but nothing spectacular. Keio's is average and its location isn't great in Tokyo... Ritsumeikan's exchange programme is fine but location isn't ideal unless you like the countryside and don't mind not being close to the city centre. Kyoto's transportation system is generally quite bad...
Wherever you go, you want to feel that your Japanese is improving, that you're receiving support and that you're making a good investment. Your main priorities are improving your Japanese, enjoying life and taking care of your health.
Personally, I went to Sophia University in Tokyo by recommendation of a close senpai. When I was there I undertook extremely intensive 3 hour-long Japanese language classes from 9.15am to 12.30pm with tests and homework everyday 5 days a week for 1 semester. In my 2nd semester, I was in regular classes with Japanese students for lectures and tutorials on courses like modern Japanese literature or American Victorian literature, politics and philosophy all of which were conducted in Japanese. Each lecture/tutorial was 1 hour 30 minutes long of just constant non-stop extremely advanced Japanese and all of the course material/secondary reading (on Darwinism, for example) was in Japanese and most of the novels I read for my Modern Japanese Lit class had never been translated before so I was reading around 2 dense novels on a weekly basis. I also had to write weekly essays for each subject in Japanese of about 1500 words long, never mind the end of term essay for each course that was triple the length. Even all of my exams were in Japanese where I had to write essays on Social Darwinism or discuss how examples of some modern Japanese texts were political critiques of the Second World War and the Japanese regime at the time.
Sophia University was also amazing for pastoral care. For example, counselling, doctor visits, literally anything. Other universities might end up just saying, 'try your best' even if something serious happens.
Pastoral care should not be overlooked when considering where to go on exchange.