Danny,
To answer your question; I think the microfilm publications having to do with the war will eventually be digitized and placed on-line either on "Footnote" or some other site. I heard just recently that footnote had been sold so who knows what their direction will be. In talking recently with the people at Archives, it is clear their dirction is to reduce the traffic coming into their facilities. The above strategy is and will continue to accomplish that end goal.
You are aware that "most" of the microfilm publications are available from LDS. One exception is the "Letters received by the Confederate Secretary of War," microfilm series M437. They have the index rolls, M409, but no letters which doesn't make a lot of sense. In any case, I am working now with LDS to try to get them to purchase the M437 microfilm series.
You are also aware that there is additional unpublished microfilm concerning the TM at Mullins library in Fayetteville. This film almost had to have originally come from Archives but I have never been able to find a reference to same in the Archives listings of microfilm publications.
Last fall, I spent 7 days in Archives. I took my travel trailer to a nice campground near Cherryhill, MD which was about a quarter mile from a Metro train station. The metro has a station across the street from Archives. So, it was a fairly convenient and affordable way to get to Archives to do research. The only problem was that it took three days to get to Maryland and three days to get back home. But then, what do us retired guys have but time.
Hugh Keen