I have worked extensively with Jetspeed 1. I have been a bit out of the loop since J2 and JSR 186, but here is my best guess. It is only a guess, but I'm confident enough to post it here.
(Assumption: a portal uses a portlet container, and a portlet container cannot really run by itself.)
Jetspeed 2 aims to be a full enterprise portal which uses Pluto as the portlet container. Pluto has its own simple portal, as it does not want a dependency on any given portal project. I believe the Pluto portal is not intended as enterprise-level.
The statement above is supported by this part of the Pluto FAQ (from here):
Is Pluto an Enterprise Portal?
No, the Pluto project aims to provide a Java Specification compliant
Portlet Container. In order to support
the container, the Pluto project
provides a simple portal, however,
this does not provides optional
services such as single sign on. If
you are looking for an Open Source
enterprise Portal implementation,
there are several available. Apache
Jetspeed is an enterprise portal
hosted by the Apache Software
Foundation. Sakai and uPortal are both
educational portals which utilize
Pluto as their container. There are
many other open source portals.