To return the nutrients to the land from a major city would require substantial logistical support - a more challenging problem, unless one can decentralise the cities themselves (and in some respects - eg energy use - cities do have their efficiency benefits).
Funny you should say this. Modern waste water treatment systems do end up with some "material" that is not digested by the bugs in the system (and indeed, billions of dead bugs themselves)--typically called sludge. This is periodically removed from settling ponds, pressed dry, loaded into trucks and spread on ag fields as "biosolids". It is tested for water content, metals and pathogens, but it is most certainly a back to the land movement! 
I actually noted that in one of the earlier posts responding to the resident troll (which I usually manage to avoid) - that even in the modern system some portion of treated sewage waste ends up on the land.
There are a lot of things that it isn't (and cannot) be tested (or treated for) and I think I'd argue it's an imperfect and out of date system that hasn't really been changed much for several hundred years (actually some of the sewer systems in major UK cities literally date from Victorian times like some of the rest of the better (longer lasting) infrastructure.
It's also an issue that a lot of stuff is discharged back into rivers (or the sea) - sometimes in a semi controlled manner where it is treated first, and sometimes in an uncontrolled manner when excess rainfall causes storage facilities to overflow (this happens with increasing regularity in the UK such that it is no longer really exceptional).
This is of course another impact we can expect climate change to have on sanitation infrastructure - during times of increase drought it will be harder to find potable (or even non potable) water to pour down our drains with the waste and during times of flooding it will be harder for both the treatment infrastructure to handle the waste without releasing large amounts untreated back into the surrounding environment.
Inasmuch as dilution is the cure to much pollution that is one of the big problems with modern systems.
However one drawback I note with most of the small scale composting systems is the requirement to add biomass (eg sawdust or straw) into the system. Could that realistically be scaled up on a city wide scale? Is there any alternative biomass that would be more environmentally friendly (particularly to replace sawdust considering how slowly trees grow)? How would one transport the compost around from household to a centralised distribution infrastructure? (why couldn't it be like taking "out" any other type of trash though, besides western squeamishness?)
I'm also not immediately sure about economics of scale with composting bacteria that produce heat - too much heat and they might cook themselves. Given heat loss is a function of surface area where heat production is a function of volume that is likely to introduce constrains upon the size and capacity of individual composting units (just as it limits the body size range for mammals).
However, I understand it is possible (and believe some canal boats - barges - do precisely this) to set up a continuous flow process where waste enters the system at one end and garden ready compost exits at the other. I have heard good things about composting toilets on sailing boats but 1) we just dump at sea usually 2) I'm not convinced most of the people I spoke to have enough capacity to truly let the waste go all the way to compost (they mostly like how it gets around inspections by various authorities who want to verify they aren't discharging within the prohibited range from the shore).
I think one thing touched upon already but worth emphasising is the scope for biogas produced from human wastes - if it might be more efficient to firstly generate gas from the effluent and then to compost or return the residue to agricultural land. Here obvious questions are what compromises are being made - is the mode of decomposition and the bacterial population different in ways that might cause concerns? (methane is released by anaerobes and my understanding is compost needs access to oxygen to work properly).
Around this point we reach the limits of my meagre knowledge on the topic, I'm afraid to say.
I decided to just dump to sea for the immediate future (I have nowhere to properly grow food atm), and besides minor experience of composting in relation to growing vegetables and food in the past and my interest in the question of sanitation and implications for future civilisations (a civilisation emerging from the ashes of collapse is not going to have either the resources or desire to make their first priority the construction of a modern (Victorian tech era) sanitation infrastructure) - that's as far as I've gone to date.
