Out of all the main Mario games, Bowser's role in Super Mario Sunshine was probably his strangest ever. He doesn't really show up until the very end (his son Bowser Jr. was more of the antagonist at first) and is more sympathetic than his previous incarnations as a heartless monster.
I will have to say the lava area getting to the Bowser battle was one of the most frustrating things in the entire Mario series. I only managed to get through the volcano a single time.
The final boss battle is one of the criticized in the whole Mario series. Mainly because all you have to do is rocket stomp the arena four times while Bowser and his son barely posing a challenge. I liked it though, the rocket stomp was really cool from that height.
It was also the first game were Bowser talked past a sound. Bowser basically told Bowser Jr. that Princess Peach was his mother, and at the end his son realizes that his father is a liar. Leaving us with a rather unintentionally hilarious conversation.