Some bus stops are located way too close to each other in my opinion -
That is just a symptom of the service frequency being too poor. If it's been long enough since the previous bus that the crowds have built up and the bus has to stop at every stop along the route, there should have been one or two buses in between to take some of the load.
For all we know, this plan might have dealt with that a little on the core routes by increasing frequency - but we'll never know which routes were to get upgraded because we never saw the details. For all we know it was just going to be a net cut in services (all the routes to be removed) with no or little corresponding increase on other routes.
Now it's probably true that there are some routes
that are too close together, which could be merged to provide a better frequency on one route, but that's something that can still be done on a case by case basis. I wouldn't expect to see this any time soon though (and certainly not until there's a new transport minister) as it would cost too much political capital after this fiasco.
The renumbering plan was pretty sound - though I would have gone for all the city routes with two digits having a C prefix for normal services and an X for peak expresses. Hopefully this part of it will be kept in mind for the future when it might become politically acceptable to have another go at a better bus reform plan that doesn't make so many cuts.
Taking ownership for cancelling the plan was one of the smartest moves that Steven Marshall has made as premier, not least because it made the first half of a 1-2 with the next day seeing him cancel the opening of the Victorian border. He could probably go a long way to winning the next election by opening a public consultation on firing Stephan Knoll.