I think Kilika and Macalania are quite well designed. Kilika is extremely straightforward until you reach the last room with the fire. There's the same glowing glyph on the floor as there was in Besaid saying "push me here", and the bright red line flowing towards the fire from the other sphere is pretty suggestive that it's partly causing the fire. Nothing that a bit of thinking couldn't solve. Macalania takes place entirely in one room and centres around one puzzle (rebuild the bridge). It's a bit complicated to get the Destruction Sphere, but solving it to advance isn't too hard.
Djose's gimmick of powering up the sphere would've been okay if the game told you how to do it (IMO). As for Bevelle, the puzzle itself is fine, but it's so slow with all those animations.
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Who knew the Rivalry Rumble would be so predictable? SuperNiceDog, that's who.