Wrong date format in the menu bar

This is the new behaviour in Yosemite and it can't easily be changed. The menu bar format now doesn't read your custom format and instead displays a barely customizable format instead. The only available options for it can be found in System Preferences -> Date & Time -> Clock.

One thing you could do is use a third party utility like Day-O, which is free and does exactly what you seek -> https://shauninman.com/archive/2016/10/20/day_o_2_mac_menu_bar_clock.

If you want things more natively, you could try editing the corresponding plist file directly (com.apple.menuextra.clock). I haven't however had much luck with it.

Open Terminal and type the following:

Reading the current settings:

defaults read com.apple.menuextra.clock

Setting them:

defaults write com.apple.menuextra.clock "DateFormat" 'EEE hh:mm a'

Or 24 hours format with the (day of the) month and seconds:

defaults write com.apple.menuextra.clock "DateFormat" 'EEE d MMM HH:mm:ss'

Then refresh the menu bar using:

killall -KILL SystemUIServer

Using w you should be able to add week number, but I haven't had any luck with that and it keeps resetting the week number.

Day-O 2 is the best app for this IMO. https://shauninman.com/archive/2016/10/20/day_o_2_mac_menu_bar_clock

If you uncheck "Show Icon," it's basically identical to the default widget.