You're correct to identify the point of libraries like Weka and Mahout, which are both written in Java, as providing a solid framework for interaction between and among your program and other algorithms. However, Java isn't the right solution for everyone. Moreover, in Weka's case, the GPL licensing may not comport with everyone's requirements. Mahout's license is more friendly to proprietary software, so it's admittedly a non-issue there.

I agree that hadoop is certainly not a toy, but using Mahout on hadoop clusters works better for analyzing large data sets that you've already collected and pre-processed. If you're doing any kind of active learning, or are designing software to run on a client's computer based on feedback that they provide, mahout probably isn't the best choice.

In the end, it requires understanding your problem completely enough to justify your decision.