Quite a few changes the sequel made.
Medicinal berries are now discrete objects. This is nice because now you frequently have the ability to find them in chests. It felt a bit awkward in the first game that there is a button dedicated to healing with the berries, but they also made it semi-difficult to stock up. Towards the end you need something like 16 to fill up. And that's frequently a lot depending on what you are doing.
I'm not sure if it's actually true but it feels like they made humans more difficult and I'm not really a fan of that. At the very least the face masks make them more difficult. It felt like a nice change of pace when you had lots of enemies that were incredibly easy to take down individually. But that feels a little less true here.
Items are now hidden during play without focus use is a neat touch.