So, I sampled three, hopefully different examples of existing frameworks. Two made by me, one by Rumble.
Lets start with Rumbles BoL (Barbarians of Lemuria IIRC) framework. It has low automation (as in GM and PC have to handle stuff by hand) and is classic, as in token related macros are on that token. GM macros are campaign macros. There is a tool/button bar for most important functions.
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Next my heavily automated
savage worlds framework. All data and action is based on the character sheet. There is a frame that holds all combat related macros (switching of states, advancing initiative, run reload) and a target selection frame.
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Last example is something quite different. It is my framework for the indy game
Dogs in the Vineyard. Its a story game and it resolves conflicts by throwing a pool of dices (traits gives you more dice) and raise&see in a poker-like narrative "discussion". All the traits used to fill the pool are shown on a character sheet and your dice pool and all functionality to raise and see is in another frame. For the GM it is interessting to open different char sheets and pool windows at the same time for different tokens/characters.
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I dont believe that dockable frames are the only way to achieve this flexibility. If I - as macro coder - can place my content on a thingy you call layers, its all fine by me. I dont think that macros are easily stored in context menus (maybe radial?), because the space is pretty limited. I might have, in a complex framework, lots of macros on a token, easily 20 or 30. Have them all float around my macro would be horrible clutter. I can see this done right, too ... this comes down to details.
Btw ... there was a huge thread about UI changes some time ago where a lot of cool ideas happened - stuff like corner menus, radial context menus, transparent layers, ... . Have you (username) read that?
I do like the ability to place my framework windows tidily on the screen edges (eg character sheets) or have them floating (eg toolbars or dialog-style windows like click based attack dialog). I tend to use different layouts for different frameworks and it does matter if i play or GM.
EDIT: oh, if you have questions to how the frameworks are used, feel free to ask. I think it is important to get a good grasp on the workflow and the screenshots might not suffice.