I assume that there is some type of application for which NetBeans is as good as (or better than) Eclipse - that application is NOT desktop/standalone Java application.
As someone that maintains a java-based emulator for several years I couldn't disagree more with that.
As a long-time Eclipse user, I moved to NetBeans for just short of two years before the delay when starting an application and the very flaky dependency building (when multiple projects are included in the final application) drove me over the edge and back to Eclipse. In Eclipse you hit "debug" and it starts debugging the application. In NetBeans you hit "debug" and it starts to compile. Change code in Eclipse, hit save, and quite often the application continues with the new code. In NetBeans the on-the-fly debug changes are unreliable and slow (another compile cycle).
Then you are doing it wrong, dude. You should make sure to check "Generate debugging info" under the compile settings for the project, which eliminates the need for the IDE to do it on-demand later. You can connect the debugger to a running instance by clicking "Attach debugger" as long as the process has JPDA enabled already. I do it all the time when I do J2EE or Sling-based dev work since the app servers I run locally have JDPA enabled for that purpose. If you're debugging a desktop app then, yes, you must tweak the parameters ahead of time, or just remember to run with debug instead of clicking "run", but that's minutiae and can be easily resolved by a little self-organization (e.g. decide if you are debugging or not before you launch the app) As for the flaky dependencies, were you using a Netbeans-defined project or a Maven one? If you define your project as a maven project then not only do you get simplified dependency management (which I use without any issue with both large reactor project structures as well as sibling-level dependent ones) but you also get CI support for Hudson/Jenkins. Incidentally, Netbeans can talk to Jenkins directly if you configure it to do so. If you were using a maven project structure and you still couldn't get it to work then you might have been doing something wrong (or just violated the KISS principle somehow.)