1st of all.... I agree fully that it is a complete and utter mess!
In effect the major problem is that there are brand new bits of route {canal tunnels/ remodelled London Bridge- Blackfriars} so, in part, are the problems due to late running engineering works?
and of course, these new bits of route are at key locations in the network!
this isn't probably the place to ask... but if there are key points where there is a problem why don't the TOC's announce a blockade at weekends with Rail Replacement buses so they can release drivers for intensive route learning?
No, the infrastructure was there in time. The TOC did not get sufficient drivers either trained or qualified on the relevant rolling stock or routes in time.
Because driver shifts work in such a way that a different set of drivers are working each weekend. You would need at least three weekends of blockades.
Also the the relevant routes all carry trains from other operators. It would be way too disruptive.