First, clicking on a location didn't set the cursor. Especially when editing large files, I like to scroll in MacVim, click to set the cursor and then start typing. While I can do things like note the line number and jump, or scroll by moving the cursor with key commands, I find those less efficient.
Second, selecting text using the mouse didn't produce a selection that Vim knew about. I use this feature all the time in MacVim, to produce a visual selection which I then rewrap using `gq`, filter by piping the selection through an autoformatter like `rustfmt`, etc. Again, I can do this using keyboard navigation exclusively to make visual selections, but I find it easier to select using the mouse.
This seems to be something in Vim rather than a NeoVim-specific setting, as I tried the same thing with the standard Vim and it worked the same. The scrolling feel in the Terminal isn't as smooth as MacVim, but it's still pretty good.