You may want to enable that “Show toolbox…” checkbox in the preferences. Right-click will show the toolbox as a horizontal bar and select the tool upon mouse button release. Both Ctrl+Right-click or Shift+Righ-click (on Windows, so Cmd should work on Mac) will be opening the context menu with the rest of the options. You won’t need to go to a submenu to access the toolbox. The context menu seems organised somewhat better, but I cannot say which commands you use most commonly. The context menus are not customisable.
Personally, I’m only using keyboard shortcuts for commands and tools. Start using one new shortcut every day, and in two weeks you’ll forget that there even is the right-click menu.
It’s unreasonable to expect that any software as complex as Cubase wouldn’t change in 11 years, and even less reasonable that it would also somehow change at the same time (otherwise, you wouldn’t have upgraded it, because why).