The controls in SMS were partially saved mainly because of being able to use FLUDD to compensate for the vast majority of missteps. That said, you are 100% right when it comes to the bonus levels where Mario loses his access to FLUDD. In this case, I agree that the controls can become quite frustrating and is one example of where the game really ceases to be fun. Also some of the bonus levels (e.g. the pinball machine level) is completely broken which is very surprising to see come from Nintendo, much less in one of their flagship titles.
Sunshine was not a great game, in my opinion. It had some fun moments, but a lot of the time I found myself just playing it so that I could complete the game and then move on to something else. I know that Nintendo was trying to take Mario 64 to the next level, but the more intricate platforming and puzzles just felt tedious most of the time. FLUDD was clearly inspired by Banjo Kazooie and it even looks like a creature hanging on mario's back similar to Kazooie in Banjo's backpack. That said, I just thought that the BK did a better job with the dynamics of a tandem platformer than Sunshine did. The best part of Sunshine, I felt, was the final boss which actually wasn't as tedious as I was expecting it to be after some of my experiences collecting the shine sprites.
That being said, after finishing Sunshine, I moved on to Skies of Arcadia. I can tell you that I had at least 10 times more fun and made probably 100 times better memories playing this game than I did with Sunshine. It's far more worth your time if you are spending time gaming on the Gamecube.