I think the focus should always be on the chat window, where \'/\' is for emotes/chat commands. Everything you type on the keyboard goes there.
Game commands are all using a \'ctlr\' or \'alt\' + another key combination, to make them different from chat commands (if you\'re in the middle of typing a sentence in chat window and hit \'clrl\'+key, you execute the game command, but as you release \'ctrl\', you can continue chatting from where you stopped).
The \'F1...12\' keys could be shortcuts defined during the game by the user, i.e. \'say help to all guildmembers\' (chat string) or \'eat the Amazing Salami of Foresight +3\' (game command).
In alternative you could use marking menus: context-sensitive menus activated by i.e. a continued spacebar hit. Some parts of the marking menus are fixed, some other parts are customizable. This marking menu doesn\'t make a complee sense if you haven\'t seen them in action, but they work very well. Refer to the new pop-up menus used by MAX or the standard A|W marking menus to see what I mean in action.