I'm not sure what you're suggesting here.
Are you suggesting that the work at Waterloo should have been done on a protracted basis a la London Bridge, where the travel inconvenience endured by passengers has extended over several years?
Or perhaps you meant that the work at Waterloo didn't need doing at all?
From what I've seen and experienced first hand on my frequent visits to and journeys through Waterloo over many years, it's a piece of work that is long overdue and 3 weeks of inconvenience is a pretty small price to pay. The timing of the work has been well known and publicised widely for the best part of the past year.
The planning by both SWT and Network Rail, from what I've seen and experienced, has been pretty well done on the whole.
The only questionable aspect of all this has nothing to do with SWT or Network Rail, but rather the micro-managers clowns at DaFT who insisted that the franchise change takes place smack bang in the middle of the work. That piece of planning is priceless.