The platform is becoming more complex and the setup and configuration is growing as a result. The ability to create tools and products that help streamline, standardise or templatize, certain configurations is becoming more compelling. Effiectively creating tools to extend the Setup menu is one use case. Another is to allow ISV's to develop UI's or post install scripts to update subscriber editable items like layouts and picklists.
Apex Describe provides some read only support, along with the ability to query certain objects, like ApexClass, ApexPage etc. It would be good to have an API simalar to that of the existing Metadata API available natively in Apex. There is an open source wrapper
around this Salesforce SOAP API, which has become quite popular with developers wanting to develop solutions such as those above. This library however is subject to HTTP callout and requirements around needing pre-configured Remote Site settings (for Saleforce servers), so is not ideal.
Please consider making a Apex 'true to the core' API for Metadata availabe.