The project has a situation which can be described as: a portal application has to be built. This is expected to be home for many existing non portlet applications (some are Java EE based and some not).
Obviously, portal will provide SSO. Options of rendering a non portlet application to portal seem to be using either an iFrame or a URL redirect. In either case, it looks like the request has to pass through the portal server (??).
What are the challenges that this solution face? Best practices to get this implemented?
This is what a Portal solution has been meant to provide: central point of access to applications, services, people, processes...
There is also the third option for integrating legacy web applications (I assume you are asking about WebSphere Portal Server) and that would be "Web Application Integrator". You can find some info on it here
Challenges with this solution would be related to: 1. SSO - there could be some complications with this, depending on infrastructure. 2. Look and feel uniformity - Portal themes should be appropriate for web applications to be integrated. 3. In some cases Web applications will need to be changed in order for integration to be possible.
Yes, each request will need to pass through Portal Server.
Hope this helps..