Aside from megamods, I totally agree with the concept in theory. The real problem is silent hunter though.
For example, while it will work great if you're just changing a couple of dds files, what happens when your standalone mod edits menu_1024_768.ini or one of the games many sim files?
It will basically mean that you have to maintain a version of the mod for every megamod that you want to support, plus one for stock. It will also not be interoperable with small mods that require the same file unless you maintain a version for all of those as well which will lead to exponential growth on the number of version you need to support. If some of those mods are your own, then the temptation to merge in order to reduce workload is overwhelming.
Basically the silent hunter mod structure is crap. The only real solution I can see is to include clear instructions for manually implementing the mod, which some mods do. I don't really see a lot of people having the inclination to actually do it though.
There is one other way, and that would be to make a patcher program that can make the necessary edits to all the files. All mods would then be required to provide instructions that the patcher can understand, instead of direct file replacements. I have the skills to do that, but don't have the time or inclination so I won't. It's possible that somebody else will, but I very much doubt it.
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