Apple was a deeply, deeply dysfunctional company at the time. Every division and manager was fighting a war of it's own.
This was reflected in their product lineup (a million products confused and overlapping - since they were each thought up by different divisions) and OS strategy (a million technologies, sometimes innovative, sometimes not, that didn't work together).
The sales organization was also extremely dysfunctional and was busy stuffing the channel as hard as they can so each sales division could make their quarterly numbers, and then the company was saddled with massive unsold inventory when it all came back.
The reign of the previous CEO, Spindler (best known for launching the MacOS clone program) was even more disastrous https://lowendmac.com/2013/michael-spindler-peter-principle-...
Amelio managed to identify most of the issues and their source, but he was pretty helpless to actually resolve them, since the managers in the company were so defiant. He was some outsider brought in by the board, who was he to dictate orders? It took someone with the balls and the clout of Steve Jobs to actually swing the axe on people.
Amelio planned to rationalize down the products to a few simple lines (but he was only in the company for 18 months so nobody on the outside actually knows how well that would have worked). He also tried to get the sales org to stop stuffing the channels, it worked for a few quarters and then they went back to their old ways. He started the process of spinning out Newton (when Jobs came back he just axed it outright even though it could have survived on it's own without burdening Apple)
That said, a long-term Amelio CEOship would have killed Apple - all his ideas for the future lined out in his book were 100% the wrong things to do (things like doubling down on clones). He was completely clueless as a visionary.