Durga, Thank you very much for your interest in the ArcGIS Pro SDK. We have attempted to address many of our users questions w.r.t the Pro SDK in our ArcGIS Pro SDK FAQ which can be found at: http://github.com/Esri/arcgis-pro-sdk/wiki/FAQ . We will continue to update this FAQ across future releases of ArcGIS Pro.
With regards to Engine vs Runtime, Runtime is absolutely a replacement for Engine. A comparison of the two products and related discussions can be found here: ArcGISEngine vs ArcGIS Runtime Q&A
With regards to the future of these products please consult the product lifecycles which can be found at: http://support.esri.com/en/content/productlifecycles
For example, notice that 10.3.1 is not retired until December 1, 2020. That means that the corresponding SDKs for desktop 10.3.1 (Arcobjects, Arcengine) will follow the same support plan and lifecycle (meaning that the 10.3.1 releases of this product are not retired until Dec 1, 2020 also). Runtime likewise posts its lifecycle documentation there too. When 10.4 is released it too will have a lifecycle which will include the ArcObjects and ArcEngine. Likewise for 10.4.x and so on.
On the choice between Runtime and Pro, they serve different purposes. Runtime is, by its nature, a development product. It can be used to write applications from scratch or embed Esri technology in GIS and Non-GIS applications (whether on mobile, tablet, desktop). Pro is an application. It's functionality is dictated by its feature functions ~however~ it can be extended with its .NET SDK (or automated with its python SDK). Customization of the desktop platform (and, to an extent, Server platform) continues to be supported with ArcObjects.