Google it would seem, has enough faith in the longevity of the Adobe Flash player that it has decided to integrate the plugin into the browser itself.
If you download the latest release of Google Chrome from the developer channel v 5.0.360.4 you will be able to enable the internal build of Flash Player 10.1 beta 3 (10.1.51.95) by using the command line parameter "--enable-internal-flash". A plugin manager has also been added in this latest release. The plugin manage is accessible through the "about:plugin" location, and will allow one to disable plugins from loading on all pages.
The plugin's integration into the browser will alleviate many security concerns, since the plugin will now be be better managed by the browser, and will be automatically updated with Chrome itself as new versions of either browser or plugin come out.
Google, Adobe and Mozilla are part of a joint effort to create the next generation of browser plugin APIs which would overcome the current limitations and provide a more consistent, and stable experience across browsers and platforms.
Currently, even the Flash Player plugin suffers from incompatibility issues across operating systems as the plugin is greatly relient on platform or browser specific features.
The new specification for plugins has been developed keeping in mind some of the developments in the way plugins are used and handled by browsers, especially with reference to native access and out of process execution. The new API aims to be browser and platform neutral so as to minimize inconsistencies. The end result is better performing and safer plugins.
The HTML specification even with HTML5 cannot implement every feature provided by the large number of browser plugins out there. There will always be features which will be available only through plugins. While for developing something like QuakeLive, the developers would have needed to wait till a number of specifications such as offline support, local storage, webgl, HTML5 etc would have become mature and widespread -- something which would have taken a decade, by using a plugin, they could have the game out today.
Clearly plugins are here to stay, the best that can be done is to make the browser plugin experience as smooth, stable, and simple for the end users as possible. While some have opted to abandonthementirely, it is nice to see some effort being put in to the future of plugins from the browser side as well. Perhaps with better understanding between plugins and browsers, some of the common headaches involved with plugins will finally come to an end.
Here is what Adobe has to say on it's new Flash Player team blog.