I want to remove all cheesy, overly easy and glitchy ways to hunt animals. This is because I find a lot of enjoyment in killing animals the fair way, but then I miss out on the bonuses of doing it the easy way.
Issue 1. You can attack animals through cliffs and by only attacking in between their "twitches" (attempts to pathfind) the animals can't attack you.
Solution 1. Make animals pathfind around cliffs of any size.
Solution 2. Make animals walk/jump/climb over cliffs.
Issue 2. You can aggro an animal in one level and enter another level such as a cave or a house without dropping aggro. When you are in that other level you can put up defenses but not have to worry about being attacked. Stepping into the animal's level will then allow you to get a few attacks in before going inside the other level again to repeat the process.
Solution 1. Make animals drop aggro when entering other levels such as caves.
Solution 2. Only allow a player to put up defenses when the animal is visible.
Issue 3. It is possible to safely kill an animal by waiting for it to try and pathfind ("twitch") whilst sitting in a boat in deep water. As soon as it twitches, move onto the shore where the animal is, attack it, and then move into the deep water with the boat again.
Solution 1. Give animals the ability to swim.
Solution 2. Make animals pathfind more often, as in every second, or whenever the player moves.
I know some or even maybe all of these things are difficult to fix but I haven't heard from Jorb or Loftar if they want it the way it is or if it's too difficult to fix.