I'd say it's a nightmare, but a nightmare would be an improvement.

Basically, you have to learn to mod and pick through thousands of files, altering a few hundred of them along the way.  The galaxy stuff will need merged, a major pain in the ass.  The manifests will need to be altered to account for the merged assets.  Only some assets can be merged in, you'll need to modify and exclude others because of conflicts.  Simply copying them all over won't work, duplicate planet entries for instance.  Weapon entries will end up conflicting, resulting in phaser firing corellian corvettes or something.  The string file will be a nightmare all by itself, so will the graphics.

If you actually want it to not be ass when you're finished, you'll have to do a complete overhaul on balance as well.  As an example, if one were to mix ST:SOA2 with SW:Interregnum, the Federation would be able to wipe out the Empire without bothering to do research.  There are over 3000 entity files in SOA2, filtering through these for balance needs will be an undertaking.

Once you do all this, you'll probably hit the memory limit and crash anyway because quite a few of the mods already require the 4gb switch to run.  I'd either need a CT scan or a shrink if I even contemplated doing this myself, and I already know how to do everything I'd need to do...

Visit a local psychiatrist's office.

More seriously, get Notepad++ and Zombie's validator tool.  It's too much work just to explain all the work, but with a real text editor that handles proper searching and replacement, and a way to find your errors, you can get started learning.  You need to dig into your desired mods and figure out how everything works, it's the only way you'll manage a project this big, ground up.

Explore first, but once you think you know how abilities, ships, etc, all work, merge things in slowly.  Check for duplicate file names first and alter them and their references to be unique, then you need to hunt down the duplicate functions within the mod and figure out how the hell you're going to merge those together.  Only when you've done that, would I start merging them together, starting with research and ability files and then adding in one side at a time and getting them working.