Dan Steinberg mentions:
Vincent's post about the dependence of Sun tools on NetBeans seems to imply why Sun is not prepared to fold or merge NetBeans into Eclipse.
Indeed, Sun's own Rich Green has talked about Sun's concerns of that they not "abandon the constituents" (users) of NetBeans. Green also expressed his concerns over IBM's domination of the Eclipse project.
Gee, that certainly makes it sound like the negotiations fell through because both sides fought about control over the merged project.
So, even with these nominally open source projects, to the people/organizations involved, it's still all about who's the boss.