I can't find any of the Elton John interviews where he talks about Michael. But on a defunct BBC show called Liquid News, he spoke about Michael two time in 2002, very bitterly just saying he used to know Michael and feels very sorry for him. Then he appeared on the SO Graham Norton Show, and Graham Norton asked the other guest Kim Wild what it was like to tour as Michael's opening act on the Bad Tour in 1988. She said something like she only met Michael once on the tour, and that he was quite shy or reserved. Elton John interjected, and said if you toured with me we would have been partying. Then Elton John said he felt very sorry for Michael, then joked "well wouldn't you look sad if you looked like that" !!!
Elton John also made a negative comment about Michael in 1996 when he married Debbie Rowe. He said something like "A lot of nutty people get married in Australia".
I don't know if Michael and Elton John had a huge falling out, or if he was pi*sed off that Michael didn't thank him for his help earlier. But Elton John may have turned against Michael because of his out of cort settlement in the civil law suit with the Chandler's. Because Elton John did say in the mid 1990's that if he was accused of child abuse by someone she would have fought to clear him name in court. But in defence of Michael he not only had a civil law suite to deal with, but also a criminal investigation against him. And his defence stragergy in any civil trial could be used against Michael if their was a criminal trial. So their was a huge catch for Michael on that.
Maybe since Michael was vindicated in his 2005 trial, Elton John may have changed his view about Michael (what ever his view is). But I haven't heard Elton John talk about Michael since 2002. Another thing is Elton John has fallen out with other stars who were friends like George Michael and Robbie Williams who Elton John also helped with their drug addictions.