Here are some of my thoughts on this topic, since it's been discussed quite a bit throughout the years:
I heard that Dynamix eventually planned to release a map editor (though I can't remember where exactly, or whether there is even that much proof in support of this). What I do know is that in the pre-release demo, there are some "leftover" resources from some sort of internal map editor (to my knowledge, the map editor that Dynamix used was embedded within the game somehow, based on the stuff I saw there and from earlier conversations with some of the game's developers). I had heard that the map editor was fairly clunky to use and as such wouldn't have been something they would have wanted to release to the public. Since the game was rushed to begin with, extras like this would have been put on the back burner.
(I'm sure security could have been a concern as well, the missions are actually executable pieces of code and as such they could do things unrelated to the game, such as harming the user's computer), not to mention that the game itself has no built in mechanism for updating maps on a user's machine).
It's probably a similar situation with the game's AI; the game engine does not support a lot of things that an AI would need to be able to work with to function (at least out of the box; we hacked in a lot of stuff via new missions). In addition they probably had to strike a balance between quality of the AI/mission and releasing on time, as with all software.
Regarding the blight faction: I believe this was an idea for Stellarwave's Outpost 3, I was never aware of Dynamix bringing this into the Outpost series.
Unused content: this exists in every game, whether it be easter eggs or just something that couldn't be finished in time (I believe the damaged rockets are used as well if a spaceport gets damaged enough for its graphic to change when a rocket is being built/on the launch pad). As far as Santa goes, it's entirely possible that this is an easter egg we haven't discovered yet (there is another reference to santa in the game, an action type for units called SantaWalking, but no one to my knowledge has figured out what, if anything, can trigger the Santa animation).
Radio buttons: This is related to the change in XP where the underlines on UI elements for keyboard shortcuts get hidden until you press Alt. If you press alt while the game is running the yellow highlights will show up. This was never an issue on previous operating systems.
Skirmish mode: I'm not aware of this ever having been a planned feature.
