Hadoop vs MongoDB MR:
2) Hadoop's MR is capable of utilizing all cores, while MongoDB's is single threaded (upto 2.4)
3) Hadoop MR will not be collocated with the data, while Mongo DB's will be collocated.
4) Hadoop MR has millions of engine/hours and can cope with many corner cases with massive size of output, data skews etc
5) There are higher level frameworks like Pig, Hive, Cascading built on top of the Hadoop MR engine.
6) Hadoop MR is mainstream and a lot of community support is available.