SharePoint Framework natively support building Client-Side Web Parts using React. Here is a sample Web Part illustrating the different pieces of a Client-Side Web Part built using React.
So you would want to build a SharePoint Framework solution with a couple of Web Parts. But then you wonder: how would SharePoint know which Web Part it should run when? With no explicit relationship between the code and the manifest, would you need a separate project for each Web Part instead?
The SharePoint Framework Yeoman generator creates a new project with one Web Part. See how to easily add another one to your existing project.
You can use Angular to build Client-Side Web Parts on the new SharePoint Framework. Here is how to get started and what to keep in mind.
Now that the SharePoint Framework is released, here is how you would build your jQuery solution as a Client Side Web Part.