Well, I went and read your link about people complaining about Moodle. Michael and from my point of view reading those complaints, its generally the tutors who should be taken out and shot not Moodle.
Proper information not being provided for students, using a really naff looking theme that doesn't work properly and so many more of the complaints are ALL issues which are easily rectifiable within an institution or even by an individual tutor.
If people don't like the standard theme that appears when you first install moodle - try one of the 50+ others which are all available either in core or as downloads from moodle's own site. Don't like any of them? design your own or pay a designer or company to create one bespoke for you (at a cost far lower than installing certain commercial alternaitives in the first place!) You can build the cost of modifications like this into your initial planning for moodle and still come out way ahead of others in the cost stakes! Take a look around at some of the fantastic UI/front ends/Themes which are in use in the thousands of institutions using Moodle for some examples.
And I really do despair when i read (and deal with in my current job and previous ones) where people state they hate Moodle/Blackboard/Canvas/Wordpress/XYZsite because the information they need isn't on there - as seems to be the case in so much of the page you linked to (rather than focussing on the UI and navigation scheme in the point I believe you were making). I hear this from students on a regular basis and have to point out that Moodle/XYZsite does not provide the content, does not set the assignments, timescales or any thing else. That is the responsibility of the tutors using it! And yes - I have dealt with exactly the same complaint from people using a wide variety of other LMS/CMS systems as well.
Personally, i don't like the default settings out of the box in Moodle, or Wordpress or Drupal, Joomla or any others I have worked with. But then neither do I see very many sites that do use those defaults without some changes.
Again as a personal opinion (and being VERY aware that others will have different opinions!), I don't particularly want to have to find a 'Return to Course' button at the end of an activity/module - what if that activity is over multiple pages or invokes the 'scroll of death' and I need/want to switch back and for between activities and my course page in the middle? I can think of any number of situations where I would not want to go to the end of an activity to find that Return to Course link. If an activity all fits on one page and I can see the bottom and there's a big Return to Course button there, I'm sure I would find it useflu - but if that activity involves scrolling down the page - very often I will have scrolled it so i can see the last line - I'm not worried about what's in the footer or anything and I wouldn't see that nice big user friendly button because it wouldn't be on my screen. At the same time that doesn't mean it shouldn't be there for those that do want it - I just don't think comparing that with other methods and saying one is right and this other is wrong and implying that it obstructs learning is very helpful.
So many matters of UI design are personal and based around what someone is used to. My own experience is that when i want to move to another page, my eyes flick back to the top left of a screen automatically - its where the browser back button is in most cases, its where breadcrumbs normally are (and I often find myself wishing a site had breadcrumb navigation to use when they dont!) and its where my eyes would go to type a new url.
I feel there is a massive case of 'what you are used to' in any design - how many people hated the Word Ribbon at first because they were used to the previous style menus (I still hate it because I'm more used to using LibreOffice) That doesn't mean its wrong/bad design, just that people took time to get used to change.
Theme designers, contributors and hq developers all work very hard to get the designs RIGHT for their users - is any website/LMS perfect? I would say no. But when a system uses a fairly standard navigation tool such as breadcrumbs I don't think we are talking about asking people to become 'Moodle experts and learn about our sort of breadcrumb navigation method'! Is there a place for alternatives - of course there is. But that doesn't mean what's there right now is bad (in my opinion!)
PS I have to say I'm not totally surprised that the site you linked to is closing - a site which appears to be set up to provide space for people to swear at and loudly complain about whatever they want (89% of all users on the site 'hating' something) and a site which has stats such as that for Sakai - 56% love and 44% hate based on 393 opinions and yet could only show me 1 positive and 1 negative comment is fairly likely to struggle to make it pay! Maybe its because I'm not signed up (and I'm not going to to such a negative site!) and yet it shows me a full page of +ve comments for Moodle and 2 full pages of -ve ones? Perhaps finding a link to a rather more balanced site (I'm talking generally not about this specific issue - one which does not appeared to be aimed specifically at 'haters') may be useful and one which focuses on the UI issues you are posting about? Preferably one which encourages a debate rather than just the spleen-venting which appears to be evident on that site. Statistics can be very useful in a debate, but when they are as obviously skewed as those on that link, they can also be detrimental to the valid points being made.