Know Your PreyThere are many different creatures in the hunting missions, and knowing how each behaves is integral to success. Some are slow but durable, easy to stalk and slay over a long distance. Others are skittish but fragile, which means that the difficulty lies in setting up the one attack that will catch them unawares. Still others are vicious predators that will actually attack the Patapons when disturbed. Luckily, every animal has a distinct appearance or markings to set it apart from the rest, so it's easy to remember which creature does what after you've gone hunting a few times.
Weather is a major factor in hunting considerations. Different animals prefer different conditions, so figuring out what weather brings out which prey is a handy skill if you're looking for certain spoils. Sometimes, you'll need to provoke the weather yourself with a Miracle to unveil certain wildlife.
In order to have a successful hunt, you need to be able to bring down your prey. Patapons with melee attacks (Tatepons, Robopons, etc) are poor choices for a hunting party, as even the most slow-witted animals will flee before they can strike. The best units for a hunt are Yumipons, as their incredible range will allow them to strike most animals long before they can escape. Yaripons and Mahopons can also attack from a great distance, with the latter also benefiting from wide attack range. However, Megapons and Toripons are a bit less effective at hunting, as they need to get somewhat close to attack a target. As such, they are best suited for prey that pauses before fleeing.
Of course, there are exceptions to this setup. For instance, Gancheeks are slow enough for melee units to attack them with impunity, and their high health means that the added power of a close-combat squad could b the difference between success and failure. In another example, the splash damage of Megapons and Mahopons can easily defeat Pekkora and its spawned offspring simultaneously, preventing the mother from going berserk and stopping the children from becoming invulnerable.
Secret HuntingSeveral hunting missions have secrets for inquisitive players to uncover. A rare creature may emerge in certain weather conditions; a certain animal may hold a special artifact; an odd object may appear along the way. As such, it pays to return to hunting missions whenever something changes (you find a new type of elemental weapon, the weather changes in the mission, you gain a new drum, etc). There's no telling what you might find!