Hidden inside bases are planned for Act 3. That's been on my planned list for a long time. These will belong to the mysterious new Archic race. though not the Replicons.
The new Rask replicons already cut your ropes when they spin. You can only grapple them for about one second. They jump and spin constantly. The Rasks are the alien dragonfly spinning things. They are deadly and kill me so often. They can jump massive distances and only need to touch Bob for a split second to destroy half his health. Fighting 2-3 of them at once is super dangerous.
Enemies that can throw things? I've considered that too, and it still might happen, but I'm leaning towards a flying enemy that throws itself. Maybe something that attacks like an eagle. We already have plants that throw things in build 0.7. The new purple planets have a seed that they launch if they detect the player. This bounces around before exploding.
"Mess with cargo"? I'm not sure what you mean by that, but trying to figure it out gave me some good new ideas.