Having lived near to Canada water for about 6 years and been a frequent user of the Jubilee Line I would say that the problems it has with capacity are similar but much less severe than you get at other stations closer into Central London. The Northern Line for example is pretty impossible to get onto at peak times anywhere between Archway and Camden Town.

The really odd thing about CW station is how big it is and how few people there seem to be in it mostly as it was built for the kind of capacity it will start to see from next year and not really for the last decade. When I lived round there a lot of people were concerned by the amount of new development that was being proposed for this area and Canary Wharf and whether it could cope and as a consequence a lot of S106 money has gone into paying for the upgrade.

Yes, the trains need the extra signalling work to cope but waiting for a train or so to pass before getting on to the jubilee line is not actually much of a delay, even though it might feel like it. At the moment I regularly have to wait for a number of Charring X trains to fill up and go before I can get on at LB.

I've said this before but it is a great station and (mostly) a pleasure to use. There are even lifts between platforms.