If the plugin system really causes that much trouble, then why was Adobe complaining about the lack of a low-level API for hardware-accelerated H.264 decoding? It would seem that they are in more dire need of a much-improved plugin architecture, so that they can outsource more of the compositing and color space conversion.
Since Adobe has tried to excuse a lot of the performance problems as due to the lack of an appropriate H.264 API, it's time for them to put their money where their mouth is. If they release a new plugin that uses this new API, and the performance is hardly improved, then it means the complaints about the lack of this API were merely a red herring to shift as much blame as possible to Apple and to distract from the real causes. If performance does increase significantly, it will mean that Flash's software decoder was shit all along, and we can move on to bashing Apple for only supporting 3 of the many hardware H.264 decoders that they ship.
The blog you link to makes it clear that there need to be major changes to how in-browser video is handled. It also makes it clear that Adobe's stance is that it is the duty of the operating system to provide APIs that fit Flash's rendering pipeline, rather than have Adobe redesign the Flash player so that it can take advantage of existing acceleration APIs. In the case of the Linux plugin, there are several different APIs that are potentially useful, but Adobe is waiting for the dust to settle and for a clear winner to emerge. Given what we've seen on OS X about how the exact nature of the APIs matters so much to Adobe, it is odd that they are avoiding participating in the open-source process by supporting a particular API and helping ensure that it will meet their needs.