There were various proposals in the late 1990s when Railtrack proposed cancelling Crossrail and running a whole variety of services via the Circle line (and other sub-surface lines). It even delayed the SSL PPP contract.
You can read about some of them here: http://www.lurs.org.uk/articles13_htm_files/03 CROSSRAIL VIA THE CIRCLE LINE.pdf
This article actually says it was so close to happening that only the Paddington rail crash stopped it: http://news.bbc.co.uk/2/hi/uk_news/politics/471250.stm
"If it hadn't been for the rail crash last week the government was due to announce on Wednesday that it was going to give the control of the District and Circle Lines to Railtrack"
I was working for LU on PPP at the time and was involved in "reviewing" this Railtrack idea. You would simply not believe some of the rudimentary issues we had to explain to very highly paid consultants who saw no issues with a Virgin Express train arriving at Baker Street tube Platform 5 at 1730 and being "alighting only" - I kid you not. Having to explain to them that the trains wouldn't fit and that it is beyond ridiculous to try to tell commuters that they couldn't board a train on a tube platform at the height on the peak was just one of many such highlights. I am sure others had other more pressing insights to share.
Having been to Tokyo twice I would say that the through running works purely because it was pretty much designed in from the early days and the Japanese spend the money and have the rigorous and meticulous approach to operation that is needed. The fact that the Greater Tokyo area is so huge means people tolerate really horrific travelling conditions and fairly basic stock on through services. I am really not sure it would translate on to longer distance NR lines where people are used to somewhat plusher rolling stock. The system is also immensely complicated - I never really worked out what services ran through on what line. You just get used to boarding different shaped and coloured trains in the central area and hope it goes where you want! I never worked out that I could have caught the Fukutoshin line from Ikebukuro to Yokohama until I got back to Ikebukuro having changed trains at Shibuya on the way out and somewhere else on the way back.
I've no great issue with Metro style rolling stock on inner suburban / very high demand routes where you need to crush people in. Not sure it necessarily translates to travelling to Didcot or Southend or Bedford if you were to start at Green Park and then expect to travel all that way on whatever replaces the 73 stock (to take an entirely random and nigh on impossible example). You only need to look at the never ending debates and rage about seat design, seat spacing, alignment with windows etc etc that fill forums and other places to see that imposing tube type stock on very long through services would be controversial to say the least.