Moderns game usually allow to remap keys and some kind of quicklaunch-bar for often used buttons. For Simutrans, both of these informations are stored in the menuconf.tab, so a player could customize his setup via editing that file.
I think it would be nice if a player could edit that file using an in-game-wizard rather than learning how all of it works. For example, then you press an unused button, the help-page concerning shortcuts comes up, listing all (?) available keystrokes. Klick on any of the written buttons, press the keys you want that action to be - and Simutrans would change the according section of a local menuconf copy.
For the menu, either use a "change menu" tool or drag&drop to move single Buttons to one "custom menu". This would be harder to achieve, since currently you can't declare single objects properly (problems with the icon showing), but I think it would be very player-friendly.