Sun missed the boat with regard to tooling: back in the early days of Java, had Sun made javac just that little bit more powerful, it could have solved many of the build solution needs there and then. Instead, people probably used Makefiles for a while before Apache Ant came along.
And the best retort to "install a JRE" is, of course, "which one?" I have to run stuff which only works with Sun's Java - it can't be anything like IcedTea that most probably implements the breadth of the required functionality - and so the practice of industry hacks targeting a single, narrow, effectively proprietary platform continues, but everyone can claim that they're using open standards.
Oh, and those industry hacks will all be working in a cathedral-style project up to their necks in dodgy code and with "security through obscurity" being one of the project value statements.
But I agree with you that high-level languages with managed environments can and should provide significant simplification over systems programming languages like C and C++. The emergence of stuff like Maven indicates that there's plenty of complexity remaining, however.