I play these games (including the PS2 games) on the regular, and what I always dread going back to are the mini games that are needlessly hard. Ship combat and the Giant Clank segments come to mind. Hover racing was always a bitch too, but at least you could beat the game without doing it more than twice ( I think?) Anyway, the variety breaks up the monotony. I get why they did it, and games just used to be designed this way. Rather than specialize, developers would take a kitchen sink approach. At least that's how it seemed.
For what it's worth, I thought the clank stuff in Crack in Time was some of the best that side stuff ever got. You kids are so spoiled. I remember back when you had to play 5 tedious sidescrolling Captain Quark levels to make story progress.