I'm in the middle of writing a "DF for Newbies" document and I feel this problem is a pretty big one.
There's two kinds of menus in DF: fullscreen and "sidebar" menus. The fullscreen menus are for futzing with general settings, and use the arrow and pgup/pgdn keys for navigation like most programs do.
The sidebar menus are for interacting with objects on the world map, and have to keep the arrow/keypad/pgup/pgdn reserved for moving the cursor around on the world map, so they use + - * / to navigate through the menu items. That's okay too; it doesn't take long to get used to.
The problem is the handful of menus which use yet other navigation systems. Unfortunately, the worst example of this is the in-game help, which is there for the sake of newbies, but which uses a confusing navigation style.
Its use of - and + to navigate through links should be dropped and replaced by the arrow keys. Pgup/pgdown should work as it currently does -- view next or prior screen. I don't think anything is lost by getting rid of the ability to scroll through these pages one line at a time.
Another big menu inconsistency is the Adventure Mode inventory menus. These are cumbersome, using * and / but not -+, nor the arrow keys, nor enter. They ought to be switched to plain pgup/pgdn/arrows to highlight each choice and enter to select.
Relatively minor is the 'O'rders menu in Dwarf Mode: it doesn't involve interaction with the map, but is a sidebar-type menu. It would be less inconsistent as a fullscreen menu, and would probably allow for future expansion better.