As of Byobu 5.x, several menu options have been deprecated, most notably the ones you've mentioned (the ability to choose your colors and set default windows).
Regarding the colors, you can trivially set them by editing the file ~/.byobu/colors or ~/.byobu/colors.tmux depending on your backend (screen or tmux). When Byobu was originally released (under its old name, screen-profiles), changing the color of the status bar was a big deal :-) But that's not one of its key features any more.
Regarding the default windows, you can also still customize those by editing the file ~/.byobu/windows or ~/.byobu/windows.tmux. In this case, the curses interface was just clumsy and inefficient. It didn't work particularly well and was difficult for me to support. It did a few things pretty well, but was not universally useful or applicable. For those reasons, I needed to deprecate that feature. Sorry!
If these are features that are blocking you or other Byobu users from continuing to use Byobu, please let me know and I'll do what I can to resurrect them :-)
Full disclosure: I am the original author and active maintainer of Byobu.
