In the more recent seasons of MITM, instead of common references of his thoughts, they were turned into rare references where when he did speak, it meant something bigger, and not only based on him, but on his whole family.
Since like most people said, the later seasons weren't mainly based on Malcolm and how he dealt with his family, but also based on the individual problems of the family members. He was never meant to narrate what was going on, but to explain his own feelings, and as his families feelings also became a priority over time, there was less need for him to talk as it wasn't only about him any more.
In fact, if season 7 (for example) was the first season, I am pretty sure the show wouldn't have been called 'Malcolm in the Middle'.