Throughout all the Zelda games their are many potions from red to blue to purple to green. In Skyward Sword they are made out of bugs, since you have to collect him for the salesman but what else is in it? It's not just juiced bugs, well I hope not... so what do you guys think potion is really made out of?
There are many different ways to make potions. You mention the bugs that were used in SS which was true of that era, but I think mainly after that they would be brewed from chu jelly. As we see in Wind Waker jelly of a red chu can be used to make red potion, blue for blue potion and green for green potion. They are brewed by the potion maker and mixed with his secret ingredients. What those are? Who knows. Fairies tears, fairies blood, fairies hearts? More likely it is Bokoblin piss and the enzymes in it break down whatever made chu jelly indigestable in its raw state.
Wind Waker shows us that Boko baba seeds can also be brewed to make blue potions.
In twilight princess the chu chus jelly can be consumed raw so perhaps an evolutionary advantage the chus of WW have developed, meant they were not nutritious in their raw form and therefore less attractive to predators.