I feel all of those problems are solvable, and it would be a huge improvement. The fact that railways have multiple lines is at least half the reason I don't want to use them. Same with the tube.
Today, using the tube is torture. Constant interchanges, deep long extremely crowded hallways, and it's getting worse every year. Why can't that be fixed ?
I'm convinced this can be made safer than central signalling.
As for the vehicle sizes, I'm sure whatever size vehicle is necessary could simply be constructed, and the article on wikipedia for mentions that you could have battery-powered vehicles with rapid charging at stations, negating the cost of having and maintaining dynamic (moving ?) electricity connections throughout the tunnels.
A vehicle the size of an 800-person tube train wouldn't be able to get round the tube corners without rails, and how could you negotiate a destination that made sense for that many people?
Likewise "operational separation" of different lines is key to reliability, both to ensure incidents on one line don't affect service on another, and because points are subject to a lot more wear and tear than plain track (see the current disruption to south London rail services, caused by a cracked crossover at Lewisham). Going forward TfL is trying to move towards a network of simple, self-contained end-to-end lines, e.g. by separating the Northern line into two independent lines rather than one line with five branches.
The kind of thing you're describing is in operation elsewhere in London where the capacity requirements make it more appropriate: http://en.wikipedia.org/wiki/ULTra_(rapid_transit)