i am not in position to argue with you considering the huge delta between our knowledge about these things, so please don't interpret it as me questioning your knowledge/experience.
I have been building megasquirt over the winter and doing quite a bit of research on it, so i'd say i am qualified to bring up some things about it.
You are absolutely correct about MS being more of a hobby ECU as opposed to heavy duty piece of hardware. But i read posts/reports from the designers themselves (Al and Bruce) that one of the most important considerations for their designs is standard automotive quality prerequisites (like for instance apropriate range of operation temps or measured ability to withstand shock, etc..).
MS2 processor is also much faster than original MS1. And all the firmware on MS2 is written in C and thus much easier to customize than platform specific assembly. And MS3 will be even faster. There are many advanced things they are considering for the next design, for instance having enough processing power to be able to do ion sensing.
The beauty and appeal of the MS to crouds of DIYers is the fact that it is highly customizable and "open" platform, both hardware and software-wise. And the MS community is one of the most knowledgeble and supportive i have seen (also very mature).
I am the kind of person who likes to tinker with stuff. Right now i am in the middle of finishing the software for PDA (running linux on it) which reads all realtime data from MS and displays it through my own custom interface in realtime (here is a video btw: http://www.youtube.com/watch?v=MWcl65SDX5o)
I don't see an easy way of doing something like this on stock, providing that everything about it is *closed*.
The recent multitude of free software that was tested by the large community allows easy tuning "on the road" with a wideband, software analyses datalogs, calculates hp/tq curves and adjusts tables automatically or under operators guidance (alternative for expensive dyno time).
Not sure when was the last time you looked at megasquirt progress, but there are also many advanced features like warmup enrichments, accel enrichments, etc. Many report with some work they were able to tune their cars to run better than the stock ever did.
Hope you are aware that the popular VEMS in europe is a commercial spinoff of MS.
But you are absolutely right about DME being the cheapest solution for a person who doesn't wanna delve into these kinds of details and just have a reliable car while not worrying about stuff blowing up.
I am sure things like MS will never eat in into the stock ECU's "market share" as they are different things for different people. Just like windows and linux. The beauty of both platforms are in the eyes of their beholders.