Jabu Jabu is very easy though.
There is a pretty nice route inside of it that works consistently and the boss fight itself is easy once you remember each phases by buffering inputs to nearly consistently beat it very quickly without taking any damage.
The only annoyance maybe is to carry Ruto around but like you can literally use her as a prop to kill enemies, hold switches down, and even hit some of the ceiling targets that would otherwise require the slingshot or boomerang to activate them, which is in my opinion incredibly dumb design but in a good way.
Water temple is only confusing if you forget that one room under the main pillar room after the water level is risen back up to get the last small key needed to visit the remainder of the dungeon.
The only real annoyance is having to constantly pause and unpause to equip boots, but playing in the decomp port adds the benefit of equipping boots as item to one of the extra dpad buttons so it becomes much less cumbersome to navigate underwater areas.
Personally I found the Shadow Temple to be the most annoying of the bunch.
It just keeps dragging on and on and it just feels like it was stretched up purely to force the player to spend the most time inside of it going through all places to fetch every small keys while racing against the clock to not waste all your magic meter using the Lens of Truth to make it somewhat playable if you didn't have the entire layout memorised to navigate through most of it blind on top of backtracking several rooms multiple times to make it more aggravating.
