Plugins options are being scattered all over the options table in no logical order nor convention. It's a good practice to keep all options in a single array for each plugin, but it's up to developer to do that. I would recommend to introduce a more conventional way of saving plugins' options. Wouldn't it be much easier to have automatically generated option key something like _plugin_$name and all options would be saved there.
It doesn't have to be exactly that way, but I think WordPress core needs to be aware of the plugins options separately from the core options, and which options belong to which plugin. This will add some order in the options table and more robustness to functionality of plugins and system overall - easy to maintain and operate.
This would also open doors for better maintenance plugins that would allow us:
- import export plugins settings easily;
- cleanup orphaned options from plugins that are no longer in use;
- new opportunities for plugin dependencies;
- bundle plugin packages with pre-setup options etc;
I'm sure there are more things that people will come up with.