Tokyo/Kyoto/Osaka – Best Hotels & Districts

Hi folks,

I've been lurking here for a few weeks now as my wife and I will be coming to Japan in July. 5 Days Tokyo, 1 near Fuji in a Ryokan, 4 days Kyoto, 6 Days Osaka and finally back to Tokyo for 2 days before flying.

I'm wondering if any one has hotel recommendations for Tokyo, and even Kyoto and Osaka.

For Tokyo, we're not interested in Ginza district. I'd even looked at the Godzilla hotel but that seems to be £400 more than other hotels. We want something fairly priced, mid range.

On a side note, what's peoples opinions on getting breakfast included? Do most people just get breakfast out?

Thanks to everyone that replies.