Thank you for all of your work on this incredible game! I was planning on splurging on the Steam Summer sale but it looks like I've got a new obsession instead. I'm a new player, only up to day 15 on Story mode, so I can't comment on the changes to the controls. I think the controls are a bit complex but mostly fine once you get over the initial learning curve.
I don't love that the number keys are assigned to a lot of inventory functions, as they aren't very intuitive. I'd prefer a context menu that I could click on or similar inputs to the general gameplay. For instance, it would be nice if holding E while the number key list is visible for an item would let us scroll through the options with mouse wheel the same way that you can with items that have multiple use actions like the backpack.
Also please consider toggle options for the crouch and run keys.