I used to visit Tokyo annually, at least, now I'm lucky if I get to go once every two years. Shibuya has been going through (is going through) a huge redevelopment and its personality is changing. I wasn't there long enough on my last visit to get a handle on why it felt different, but my gut impression was that the area is growing up.

Rather than Roppongi you might like to visit Azabu Juban, has some of the urban villagey feel that you were describing. Mount Thabor bakery is a must (home of the Hokkaido milk bread), but there are a plethora of smart, tucked away restaurants and bars and it has an open square area that feels almost Parisian (and I stress the word "almost"). Azabu Juban is a short bus ride from Shibuya.

To expound on RichardInSF's comments on Tokyu Inn/Stay properties:

If you have no intention of hooking up with anyone in any shape or form (and I didn't on my first visit but still met my husband) then the Tokyu Stay could suit you. Otherwise, go somewhere else. The more stars, the more likely the hotel will be more 'relaxed' and tolerant to any unexpected change in circumstances and requirements. It is worth making enquiries about policies before deciding. Staff in cheaper hotels seem to have photographic memories about who is staying with them.