Netduino or Raspberry PI for my requirements?
You list contains many might/could clauses, so I don't think it can lead you to the one and only board. Maybe for a specific project, but not in general.

In your shoes I would strive to become a master in the configuration (including kernel configuration, startup process etc) of Linuxes. That seems to be what you'll be using. On which board is step two, probably to be decided on a per-project basis, and likely to shift over the years.

It is a bit like asking a really seasoned programmer what he thinks is the best programing language. The less gods will come with their choice of  C, Python, Perl, C++, PHP, Lua, C#, Haskell, Ada, Pascal, and a few dozen others. The real master will say:" for this job, give me any imperative language that compiles to native code, because it must be really fast. For this other job, give me any language with decent graphics support and run-time memory management, because speed does not matter that much but my time does". In other words: the language does not matter, at a certain level some are only a few groups, and the languages in each group are almost in interchangeable.