hi Vladimir, welcome to moodle 
moodle seems to believe it can go on 'evolving' without fixing the massive underlying issue of its basic ux, but this incredibly obvious and very specific need isn't something the moodle community themselves know how to do deal with exactly because there is are no ui or ux designers in moodle hq.
It's like saying "that's bad code" to a bunch of people who don't know what code is.
Lots of the commenters are asking for where moodle can be improved, and so i thought maybe we could start a list maybe?
1. Improve the process
Make sure future developements in moodle are user friendly by testing with real users : https://tracker.moodle.org/browse/MDL-32544
https://moodle.org/mod/forum/discuss.php?d=200924
2. Give users navigation
Elongated tree views, mixing clickable and none-clickable elements, confusing labels and the ability to jump to resources without context all mixed with no transparent information architecture are a constant feature of any enterprise level cms that grows organically.
If moodle is seriously meant for learning, it needs to place the end users needs first and have an information architecture:
https://moodle.org/mod/forum/discuss.php?d=176557
Some mebers of hq are already thinking about this https://moodle.org/mod/forum/discuss.php?d=233520 - be good to move it forward.
3. Simplify workflows for content creation
Without tutors having the right tools, its difficult to create a good learning experience.
As you say “overcomplicated, counter intuitive, outdated in concept and design, hard to navigate with dozens of clicks for even simplest operations... “
“ every second click was wrong in average. If it was so frustrating for me, an experienced web guy, I can't imagine teachers on my university to do it by themselves even after an extensive training.”
That pretty much sums up the experience of every tutor i met before we started to customise moodle for the end users needs.
If anyone cannot read the above as very precise constructive criticism i’m happy to have a chat - https://plus.google.com/117151225863784084515
4. Stop looking for examples of best web practice in other vle and look for them on the web instead
At the end of the day for a student or a tutor moodle is a website.
They don’t have experience of other vle’s - they just know how to use the web. The less moodle is like the rest of this web, the harder it is for the end users to use. Restricting moodle to a ‘like other vles’ silo is damaging for the end user.
Creating forms can be as easy as http://www.wufoo.com/ - Online discussion can be as easy as facebook/twitter - Video can be as easy as youtube - Quizes can be as easy as the most fun quiz on the web - making these things complex or difficult is the enemy of good user experience, and therefore the enemy of good leanring.
I’m sorry this is all ux stuff. Moodle seems to believe it can go on 'evolving' without fixing the massive underlying issue of its basic ux, but this incredibly obvious and very specific need isn't something the moodle community currently knows how to do deal with exactly because there is is no ux in moodle.
I’m not sure the above list is in anyway the priority issues to address, but they are the things we did at sussex and it seemed to get us into a position where teachers create fantastic learning experiences without having to do an online course in how to teach, and online learning is a modern web experience for students and not a trip to web of the 90s (before they were born!).
yeh, long post - add stuff, happy for anyone to message me for more specific constructive stuff - https://plus.google.com/117151225863784084515
welcome to moodle Vladimir 