Chrome comes with bundled flash player plugin. Previously, it used to detect the other installed PPAPI plugin as well but in the recent versions it has stopped detecting it and there is a bug for this on Google's end which we are not sure they are going to fix or not. But still, the bundled plugin should work fine on Chrome and if you are facing issues on any particular website or content, please let us know so that we can assist you better.
If you're referring to the NPAPI plugin, Google is dropping support (in Chrome 45) for the NPAPI plugin and has stopped displaying it in the plugins list by default. Please see the Google support doc NPAPI plugins don't work on Chrome version 42 and higher - Chrome Help for more information and instructions on how to temporarily enable the NPAPI plugin.
If you are referring to the content debugger (used by developers) not displaying in the plugins list, this is a separate issue that we are working with Google to resolve. If you need to use the content debugger, you can launch Chrome from the command line with the argument: --disable-bundled-ppapi-flash
With the above said, please do let us know of the issues you are encountering so that they can be investigated. The best way to do this is to file a bug at https://bugbase.adobe.com/ and include information on your system (OS, processor, memory, etc), the Flash Player version, Chrome version, the website you're encountering issues with and as much information on the issue as possible.