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In addition to ctools content plugins, also look at Boxes. It uses the ctools plugin architecture to reimagine the current block system (D6/7) but is implemented as you mentioned. Box types are classes and instances of these Boxes have their own configuration making it possible to have multiple instances of any box type. They are very simple to define and also provide for inline editing. In any case, there is exploratory but production worthy work already being done on some of these areas and we would love to help where appropriate.