Good news everyone!
JaxFirehart from the Tale of Two Wastelands team has volunteered to help out with developing an installer for Skywind / Skyblivion.
He has written a successful installer that verifies the installation of Fallout 3 and Fallout New Vegas, makes changes to the Fallout3.esm file, uses command-line .BSA unpacking & repacking tools to copy files etc., and it even modifies .INI files too.
He is willing to share the code and also help with understanding it! I will leave it to him to post in this thread and update things, or feel free to ask any questions about it.
Thanks!

The installer is written in
The installer is written in VB.NET (cringe, I know). Currently the TTW installer handles files in one of two ways: it can manually extract Fallout 3 .BSAs, delete resources already found in Fallout New Vegas, and then repack them, or it can use a binary patch file to automatically just update the .BSA files. The manual extraction is slow, but also small, so download size is kept small. The binary patch is less slow, but download size is huge. The installer currently uses a combination of these two, it uses the manual extraction for initial installs and then uses binary patches for further installations. This keeps download size small and allows for quick, easy updates.
I assume that Morrowind and Oblivion files are not automatically compatible with Skyrim, so the manual extraction will need an extra step where it patches the old files to be compatible with the new.
I am in the process of overhauling the installer code to boost efficiency and make it easier to maintain. I know to know as much as possible so that I can properly write the patcher to be game neutral!