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On a huge site with 30 or more content types, and "Control formats per node type" enabled, configuration work quickly becomes a pain. Just too much work to configure each content type separately. Would be better if I only had to configure a few of them, and set the rest as "system default".
1) For each content type you can choose between "use default settings" and "override settings".
2) Allow to create different presets, so for each content type one can either choose a preset or "use system default", or "individual settings".
3) Use different presets for nodes and comments (and fields?).
On the one hand we made the configuration less work, on the other hand we can add flexibility:
4) Allow to configure allowed formats for specific combinations of node type and role.
5) Allow programmatic configuration via a hook implementation.
Now, this was some brainstorming. We don't need to have all of this at once, and maybe there are better solutions for some things..