Hopefully you are familiar with the existing WPDev UserVoice site, where you can provide suggestions (or vote on others' suggestions) for developer features to add to Windows. Note that "WP" now stands for "Windows Platform" instead of "Windows Phone," and it is intended to encompass all flavours of Windows.
We've just added an additional sub-site for Missing Platform APIs, where you can provide feedback on APIs that are available for traditional Desktop Windows apps, but not available in the Store Profile. This includes both Win32 / COM and .NET APIs that you'd like to use for compatibility with your existing code, or with 3rd-party libraries that you'd like to use but can't (because they have dependencies on missing APIs).
If there are specific APIs from other operating systems that you would like to see a Windows equivalent of, you can also suggest (or vote on) those.
Remember that, as always, providing an explanation of why you want the API is critically important as we assess what changes to make to the Store Profile over time. There are many cases where the full power of an API is fundamentally incompatible with the Store model, but a restricted use-case (or one that introduces a new capability) might be compelling.
Also, in case you didn't know there is also a UserVoice site for general Windows Phone consumer features.