Dev tools, version control tools, and any other stuff that you want to use must be standardized among all your teams and carefully chosen.

I don't think using Eclipse for big teams is going to give you much trouble as people are using it, so I guess because of its advantages that you've mentioned earlier, usually it is a good choice. I don't see Eclipse as some tool other than a dev tool, what you probably are looking for is a setup of a good version control tool which Eclipse also gives the plug-ins for that. It also migrates with RUP tools like Rational Rose. There are other tools out there such as Oracle dev tool, Weblogic, etc but I have a feeling that Eclipse has much more fans these days. Having said that having much fan is not always enough

I guess no matter what process you're using or how big the team is, how long the project is going to take, how far the milestones are, Eclipse would still be ok, even if you have C++ coding you still can use it. I started with Netbeans, Sun ONE, they are good but way too slow comparing with Eclipse. But I also agree it might be a bit tricky to set it up at first place.

It looks like you are more into comparing the tools and you have already made your decision on using J2EE. May be if you can come up with a list of dev tools that you have in mind and the kind of industry you are in, people here can be more helpful.