When I create new Windows Phone project I have an option to create a "Windows Phone" or "Windows Phone Silverlight" app. I know that they have different runtimes and different APIs. I was under the impression that Microsoft wants to unify Windows and Windows Phone platforms so why is there even a Silverlight version? What benefits does it bring? Also, if I want to create an app just for Windows Phone and never have plans to bring it to Windows, what should I choose, Silverlight or Windows Phone?
I'd suggest you go with "Windows Phone" (non-Silverlight). It's the new API, which works for both Windows and Windows Phone. At some point you may want to port the app or create a new one for Windows and you'll already know the API (and porting will be way easier). Also, the new API will most likely get more updates and features added, and at some point you may even be forced to update to it (either because the old one is no longer supported, or because it does not have some features that you need).
As it was said in the other answers - the Silverlight option is there only for backward compatibility and is likely to be phased out in time. That is - it's good if you already know the API and have many libraries (yours or others) for WP Silverlight, but if you're just starting - you'd better go for the new technology.
Edit
There is one other thing to consider before choosing between the two types of apps. Some features are only available in a Silverlight app, and others (smaller amount) - only in a Xaml app. Here's an article with some info on the differences: Migrating your Windows Phone 8 app to a Windows Runtime XAML app
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