Yes, there have been some usability enhancements since the 1.x days, but many of my original gripes about 2.0 are still alive and well in 2.6.
Repositories are a great example. I remember seeing a talk by Martin explaining that most people keep their files in Dropbox or Google Drive or Whatever, so Moodle has moved in that direction... And all of us in the audience looking at each other going, "Huh? What school uses Dropbox?" It would make sense if it worked the way almost everyone assumed it would when they first heard about it: Teachers could use their own Dropbox or whatever as a repository. But when we all realized that this meant that the school itself had to get an account with one of these services, they were turned off on almost everyone's installation. Here in Japan, it would be illegal in many cases to use such a thing.
I just recently realized that the File System Repository is just a folder you put in your moodledata folder. I.e., it's what should be the default anyway, since Moodle is just a webpage, and you should be able to add files via FTP!
With respect to the topic at hand, video, I am really surprised that Moodle standardized on Flowplayer, which requires Flash. Video.js is more versatile and just as libre/free. It is also much more easily customized. One can use the HTML5 video tag in pages and labels, but not in quizzes, etc.--but not MP4 video. MP4 video does not even seem to be fully supported by Moodle, as one has to change the extension to .flv to trick Flowplayer into playing it.
And finally, the new UI with the menus for editing has taken a very click-heavy interface and added one more click to everything, while also obfuscating functionality. I'll never quite figure that one out.
In the meantime, requirements are getting pretty onerous. I'm now hosting my department's server myself, with our own hardware, because campus network services were having trouble meeting the requirements. So now I get to drive down to reboot the server every once in awhile. This seems silly; the core functions of Moodle haven't really changed in 10 years.
I'm having a very hard time keeping my fellow teachers interested. Basically just myself and 2 others use it now; most have sneaked off to things like Edublogs (in violation of Japanese privacy law). Of course Moodle does much, much more than the competition, but most people actually don't need much, much more. The basic functionality of Moodle is some of the hardest stuff to set up and maintain.