This did boil down to where the problem mostly wasn't with the supply, right? That is, the problem was with lead pipes from the water meter to the houses/apartments? Not excusing everything the city did wrong, but I can see why that would have complicated everything and made resolution such a long process.
Then Flint decided to save money by changing water sources from Lake Huron to the Flint river which changed many properties of the water including ph. This relatively abrupt change caused the biofilm and mineral coating to weaken and expose the lead of the pipes to the water.
So are lead pipes at fault or the sudden change in water chemistry? Water chemistry changes are well know to cause these issues, the water quality chemist in most jurisdictions will be aware of the potential issues, not sure if they were ignored.
IMO the pipes should have been changed out long ago, but that doesn't absolve the decision makers from the issues caused by changing water sources to save money without consideration for the side effects.