I do not know. IMO, the CMMI-esque approach reeks of paperwork and micromanagement, and Agile approaches reek of lacking of planning. Both seem to be a bit problematic in their own way.
At any rate, would you mind providing some references & resources to read over for what you term systems engineering methodology? I am keen to understand other disciplines' approaches for getting engineering work done.
The Systems Engineering Body of Knowledge (http://www.sebokwiki.org/) would also be a good place to start. Probably quite a bit of overlap with the INCOSE site, but better organized.
OCW has a systems engineering course posted: http://ocw.mit.edu/courses/engineering-systems-division/esd-.... There are some lecture notes available, but unfortunately the materials are a little thin.
Systems engineering is especially important when software is part of a larger multidiscipline project. All discussions here seem to focus on pure software projects.