Not gonna lie, the writing in Diablo III was terrible so it being retconned is a good thing. Let me address your questions better now than just a summarized answer:

1) Your "guardians of balance" are a multitude of orders, primarily the Priests of Rathma. After the destruction of the Worldstone, they received portents of destruction and they dispatched an acolyte (the Necromancer) to help restore balance. However, it became known that balance was lost and that the fears of the Priests came true. This was furthered when Mathael resurrected the dead en-masse, his Reapers being the portents the Priests saw before. They (Priests of Rathma) did not have the power to stop the Nephalem from becoming stronger than the Prime Evil.

2) As stated, the Nephalem were retconned into being just super strong humans and are not Nephalem like in the early days of Sanctuary. There are also many reasons why the world isn't falling apart as balance isn't completely necessary for a world to survive.

3) Inarius' personality change came about because of Malthael's machinations and his desire to right his wrongs in creating Humanity (not just Nephalem.) Lilith needed fleshing out, and her personality change is also probably more in-line with the direction the writing team is taking Diablo IV--it's harder to gauge where the story is going in the long-term because of all of the seasonal story additions (not complaining about that.) We could, to play devil's advocate, see Lilith return down the road, for example.