The idea is that as a programmer, you have to have an intimate understanding of what is going on in order to make the machine do your bidding quickly and correctly.
But that mediocre Eclipse user I caricaturized does not have that understanding. He certainly knows how to get the job done for a certain set of tasks, but he does not know the details of how this is happening. Thus, he creates programs that follow "best practices", "conventions", "design patterns" and lots of automatically created wizard-boilerplate.
That might not be "bad code" mind you, but it almost certainly is not "great code", either. Thus, mediocre. And then these people create libraries that are mediocre and try to use only libraries that they can understand and that are hence mediocre. A culture emerges that is very consistent, but also very mediocre.
Hence, their code is factored just the way the IDE would, even if there are better alternatives available. This is the kind of mediocrity I am talking about. (And by the way, you could go much worse than Eclipse at that)
I actually had quite a few discussions where the main misunderstanding was that we used different tools and thus thought of different things as "easy" or "natural". In one case, one developer argued that it would be a good idea to create a whole bunch of classes to encapsulate a problem space. However, creating all these classes really would not have been necessary at all, he could have accomplished the same goal with a much simpler list of functions. Thus, we ended up with a HUGE file containing some several dozen classes that no-one but him could navigate, because it was factored just right for his programming editor but was all but unusable for anyone else.
One developer even told me that he did not know how to write a correct if statement in C because his editor had a template for that. What my argument boils down to is that this kind of behavior is bad, and I have seen it becoming a sad kind of sub-culture in Eclipse/Java land.
That said, I completely agree that if used correctly, there is nothing inherently wrong with Eclipse or Java per se.