Animals: Want to hunt for some animals? Sure, don't forget to bring... uh, nothing but a knife. Do I need a weapon? No, I just need the ocean. Seriously, don't even try to kill an animal the regular way, you won't hit it anyway. The way they move... my god, it's horrible. Basically they're clipping forward and through everything on their way.
Mining/Terraforming: "Your inventory is full? Bitch, let me try it anyway." Seriously why is that a thing? If my inventory isn't capable of holding what I'm gathering, why am I able to gather in the first place? It's so frustrating! Also, why can't I drop things in mines? Why can't I bring my wheelbarrow? Why is there so much ore on ocean level that you can't mine (extremely frustrating)?
I also don't like the fact that tunnels are permanent. Searching for iron/copper can mess up the whole scenery and there's nothing you can do about it. It's just so ugly.
The inventory: I really can't stress this enough, but... the inventory sucks. So much clicking if you want to get anything done. Constantly having to switch between tools is the worst. Equip this, unequip that, and so on.
The stacking in this game is so unforgiving. Let's say my inventory is 100/200 right now and I want to pick up 100 iron ore, but the stack is 101 ore. No, you can't simply drag the whole stack into your inventory because you can't carry that much. Seriously? Just make it divide the stack automatically, it can't be that hard.
Yeah, those are pretty much the main reasons. I won't complain about bugs because, obviously, it's still in the making. But those mechanics... I mean, someone must have thought: "Yeah, that's a good idea!"
Don't get me wrong, I still love this game. But I'd love it more with better mechanics.