I had the same feeling about Hombu, where I only went to the morning classes taught by Doshu (and one taught by someone else). Yes, it was hot and crowded and training with one uke for the whole class was limited, but the teaching style was what I found most off-putting. Doshu only demonstrated each technique twice, and I usually missed the first time because everybody was still running to sit. And not once did Doshu or anyone else come over to help or correct me. I could definitely see the potential of Hombu and the teaching style for people who stay to train for longer times, but as a relative Aikido newbie and brief visitor, I had trouble getting much out of it.
I also trained several dojos and camps from Aikido Kobayashi Dojo
and I can't speak highly enough of them. Yasuo Kobayashi and his son are amazing instructors, particularly with beginners and guests. And they couldn't have been more friendly and welcoming.
Of course it's not really fair to compare the two, since Hombu gets a number of guests every day, while the Kobayashi dojos are more typical dojos (and my instructor has a close connection with them.) But I found the contrast interesting on my trips to Japan.