the way to get around the mouse thing is to use a keyboard with built in trackpoint.
that also enables you to search for applications or select folders more quickly by typing.
i think tilling window managers(i3wm, dwm or something similar) on linux can get you quite a bit of efficiency and probably don't fuck with your configs, or at least if they do you'll be able to read it in the patch notes.
the only problem with those is that you need to run them in a distribution thats built for them or that you customized to suit them, because manjaro for example has a bunch of gui elements preinstalled that don't fit into a tilig enviroment.
from what i remember regular programs don't have any issues(i didn't get around to setting up an arch linux or whatever yet so im stuck with manjaro and xfce which works for me but definitely isn't gui enlightenment or anything).
i think a lot of the movie guis are just fantasy because the interaction doesn't actually display enough bits to tell the computer what to do.
also a linux command line is infinitely better than a dos one, most of the time there is an incredibly fast solution with the right string of commands you just have to learn them(for your select and copy example theres probably a regex fitting all of the files you want to copy).
after reading a couple of posts and seeing takes on mobile GUI i felt compelled to talk about that aswell.
Disclaimert: i don't actually use a phone from day to day and only sometimes use some experimental linux based os on an exotic phone, however that does give me quite a bit of experience with new ui concepts which i think does fit into this thread quite well.
-i don't know if it makes it faster but i really like hardware keyboards, because physical feedback makes it possible to type blindly and imo makes the overall experience a lot more pleasant.
-gestures work really well on phones and i said that before it was mainstream, spcifically sailfish os and even older maemo display great intuitive gesture control that frees up space traditionally occupied with a home button or navigation bar, and goes even further by displaying only the open application and nothing else but allows you to hold the close animation to make the application transparent and look at the notifications.
-very recently the suckless people (who are also behind dwm) released they're own phone GUI sxmo its very unfinished and at time of writing doesn't have gui settings for the modem but the general concept is a mixture of gesture controls and abusing the volume and power buttons for menus and quick actions. this, to the best of my knowledge, for the first time frees up the desktop on a phone by shifting applications into a hardware button controlled menu. a lot of the text is smaller than it needs to be which isn't great. when using the maps app gestures sometimes trigger on accident because unlike sailfish os gestures in sxmo can start from anywhere and not just the screen edge.
-another great concept i've seen in a couple of linux phone GUIs and most completely implemented in sailfish os is having all open applications on one screen with some interactivity in the smaller view so you don't need to switch between apps as much and have a dynamic selection of widgets.