Earlier quoted context omitted.
There may not be any conceptual difference, but there is a very significant difference in how these things you describe are used. Flash, when used badly, becomes a self-contained sandbox for the entire experience of a website. Besides security concerns, this approach is damaging to the overall experience of that site, since developers end up needing to re-implement native controls and functionality (scrollbars, form…
Flash, when used badly, becomes a self-contained sandbox for the entire experience of a website. But if it's rendered as part of the page instead of in a black-box plugin, doesn't that whole problem go away?
For me the best trade-off is still to use a flash-block and grant the flash running time when I choose to do so.