I'm at 1.1.12 that came with Ubuntu. These problems have been around for years: I'm glad they're fixed now (obviously in 1.1.13?) but I must say they apparently weren't a priority for the VLC developers.
I'm glad to hear that the keyboard shortcuts have been fixed, too. The super/Windows key problem was particularly nasty: you couldn't leave VLC running on the background if you wanted to use other programs.
This apparently means that as of 1.1.13, I can configure away the braindead movement keybindings. By default, I have to keep shift and/or ctrl pressed to jump around the movie. Plain left/right do what? Go to a mysterious Next/Prev or something? What's that and who uses that? Totem got the keyboard controls right here, unfortunately. Totem doesn't even need the modifier keys because right is a bigger jump forward than left is backward, so you can just use two keys to jiggle yourself to the right position.
The flickering popup menus can be reproed like this: play a movie (a dvd preferably), go fullscreen, right-click on the screen and try to navigate to some other DVD title or chapter. This involves a lot deep submenus and they flicker frantically while the movie is playing. Not a biggie but this has been there forever, too, and gives a shoddy impression of the user interface that adds up.
This is fixed in latest versions of VLC.
> Various widgets aren't standard
Which one ? All of them are standard but the volume slider and you can change it.
> The popup menus flicker when opened during a movie and they can go really deep.
I do not understand what you say.
> Changing some settings in mid-play causes restarting the movie from beginning while some settings are lost after switching DVD titles/chapters.
This is fixed since a long time.
> For example, transcoding into a file could be just a "Save as..." with a simple selection of formats.
Good idea.