GUI/UX freak here. I basically jumped the ship to Linux and started using KDE basically because of themes and ability to customize shell so I might be biased but it looks like my case is very similar to yours. I can say that I use console rarely and mostly for stuff that just objectively faster or when I have no other choice.
To answer your GUI QUEST:
What is the perfect GUI looks like:
Perfect GUI doesn't necessary have shape or form, we just have to iterate or reuse existing concept and make them better. Although I might have some concrete answers for you. See the bottom of my post, but you might not like it.
What is the best GUI we have TODAY:
I'd say using KDE on Linux, learning how to tweak it and finding the best software would be your best bet. Like LiteStep, KDE is INSANELY customizable, but unlike LiteStep, it DOESN'T REQUIRE YOU TO EDIT TEXT FILES, 99.9999% OF THINGS ARE DONE IN GUI. Seriously, you can mimic NeXT step, MacOS, Windows or nearly anything with it, and 90% of features work out of the box. I wouldn't say it has the best defaults though but you can get really far with it and defaults could be changed much easier than changing the software itself.
What is the best theme/font/icons/etc:
Again, I really like KDE, I like Breeze theme which allows you to tweak color scheme without changing the looks of it, Breeze icons are really nice too but if you like more realistic-looking icons there's Oxygen. As for fonts I prefer Fira Sans.
And now, a little bit of a rant:
First of all I'd like to address the "GUIs needs to be easy to understand" and omission of it. This is a very complicated topic and sorta part of the "There are a lot of things that are ideal for the majority of users". Mostly because majority of users are just normal people who only ever use a computer because they have to or because it's currently the most convenient way. You, Ross, yourself, complained about "learning all the hotkeys", the very same principle applies to mouse gestures, learning how to use console et cetera. This is probably one of the reasons microsoft and other companies do things the way the do. Making things simpler to understand, and often it sacrifices efficiency or other qualities, best analogy would be that Automatic Transmission is much easier to understand - it's go forward, don't go or backwards, but automatic transmission isn't efficient at its job and you don't get fine control over gear ratio and most people don't even need it. Why do companies do that? Because simpler-to-understand GUIs mean more people can use it. Nobody wants to read a manual before using something, or take special courses. More people can use means more money, it's as simple as that. Things at best are made intuitive, not efficient.
But what does "intuitive" really means? It means that you can guess how things work based on your existing knowledge of other things - you pull on that metal thing on a wooden plank and plank rotates - it's called a "door"! So let's use a door handle picture to give user a hint something is openable! That is also part of the reason windows largely remains the same across years, and why most other GUIs just copy and sometimes iterate on that? Because users are already familiar with it, and people who are have familiarity can help people who are new to the subject. Windows 8 wasn't hated because it was slower or because it has tablet interface, biggest reason was because they drastically changed things there. Imagine you move out of your house into another, and find out that doors in there don't have a handle! Then you find out they actually do have a handle but it's at the bottom of the door and it opens up like shutters upwards! Somebody thought it was more efficient that door closes on its own with gravity like that, or it's cheaper, we may never know! In case of Windows 8 it was time when people thought tablets are going to replace PCs because touch is objectively* better* than mouse! So Microsoft decided they want single interface for all of their devices and that it's ok to have that on PC too. It did work better on phones until those lasted btw. So the point is, even if you know your GUI is bad, your users are probably already used to its quirks, so the change for better must be at least three times as good to justify existing users re-learning it and getting rid of their habits. I've heard stories about people using ATMs with broken screens successfully just because they memorized which buttons they need to press in what order. Man should shape the tool but tool also shapes the man either way.
In the end you can't really rule out "simple to understand" completely, even if it's gone, its spirit still haunts the list of GUI truths, who are you gonna call, GUIbusters?
Most effecient ways? Best GUI?
However if we really focus on efficiency and forgo the "easy to understand" and other things, I'm afraid we'll have to also forget the mouse. Have you heard of Norton Commander? Or maybe FAR manager? Total Commander? DOS Navigator? Those are file managers built around having GUI in text and being manipulated with keyboard. Sometimes it's in text mode console, sometimes it's pretty GUI but you'll be using keyboard mostly. Sure these managers allow you to use mouse but interface is based around keyboard controls. Or some advanced text editors like emacs or spacemacs? I don't have to aim with mouse to click "save", i don't have to memorize that "Ctrl-S" is "save", i just hit (Space), a menu pops up, i see "f - file", i press "f", then i see "s - save" so i press "s", eventually it becomes a second nature to me - space - (f)iles - (s)ave.
A lot of software, especially in console are geared towards that and some people hate the mouse because it's, in your analogy is always an airplane, and prefer for keyboards because they're are already efficient at that. I'd say it depends on your background - if you used to such software it's easier to keep using that, if you prefer mouse - it's easier to keep using mouse as well. As you had the analogy between helicopter and plane - only ever using the keyboard would be similar to driving a manual car around town - it's probably more efficient and can't get you completely anywhere but if you have a license and know your way around town and comfortable with it - it's probably the best thing ever, as long as you don't have to travel from USA to Poland, that is. I guarantee that some StarCraft pros with 200 APM would say that mouse is the best thing ever and the keyboard isn't needed at all.
However in modern times we DO have VR and AR, and maybe it's going to change few things. I would take a look at XRDesktop, which allows you to use your VR headset to interact with your existing Linux desktop. It's a prototype and it uses existing interface, but it's interesting concept that needs to be evolved, after all, the very first cars were nothing more than horseless carriages (and they were sometimes called self-moving carriage).
Best styles? Best look?
I would say it's a matter of taste, really. However I would also say that interfaces that resemble real life objects are somewhat simpler to understand. While simplistic, flat interfaces are easier to develop. Also supporting customization always adds costs to development.
Hope you don't mind this massive wall of text I've written. I've been figuring out good GUI for several years now. I've also used windowblinds since Windows XP, rainmeter, aston (or whatever it was called) and other things trying to optimize my GUI while also trying to make it look the nices and the coolest. (Remember Windows Longhorn?)
P.S.
I've been trying to make the best interface possible on an open-source project for couple of years now. I'm trying to allow both simple usage while supporting insane amount of customization without having to read manuals. It's not quite there yet but we're getting there. The website of a project is https://pleroma.social/ and you can check out the interface here at my instance: https://shigusegubu.club/ You don't even need to sign up to try customization options.
P.P.S.
For resizing windows easier I suggest you trying AltDrag, it's a feature that's been default in linux for ages now.