Major update: 0.12.1!
I've made some important changes, and I have finally finished the large facilities! I also made it so you can tell different tank types apart by their color. The Large Hyper-wave Decoder is very expensive but covers a very substantial portion of the planet's surface.
I've added a new line of tanks which fire rockets made from Alien Explosives. These are like the laser tanks with improved armor and time units, and they are more powerful than the basic rocket tanks. It's an advancement of the alien explosive technology that I had previously added to the Heavy Cannon, Autocannon, and Rocket Launcher. The explosive weapons line is complete, offering a variety of early, mid, and end-game options for all of you demolitions "experts"!
I added several spawn points to Forest, Jungle, Desert, Mountain, Arctic, and Urban tilesets. Aliens will normally spawn in the old places, but if there isn't enough spawn points they will have new places to spawn now. This will make a big difference in higher difficulties especially, as it was previously very common to have aliens fail to spawn on large UFOs or terror missions. In my preliminary tests, I found that all aliens were able to spawn with a few spawn points left over even on the largest craft. What you'll notice is that if your map gets a lot of empty segments (just flat terrain), you may see one alien in the center of each map segment. I made every segment have at least one spawn point, though I added some extras to the normal spawn segments so it should usually look pretty normal. I didn't have to touch the Farm tileset, in fact it was so well done that it helped me understand how the spawn nodes work. Props to MicroProse for getting that done! I'm guessing they were going to put more time into the others but didn't get around to it.
Many research projects grant more points toward your score when completed now, especially late-game research. It's not a lot, but it should be significant. If you get a lot of labs and blaze through the research, you might get some very high scores for a while, and that might help improve your funding or at least pay for all those scientists.
The craft Cannon has had its damage and rate of fire greatly increased. It's still crap range, but it deals damage even faster than the plasma autocannon now. I'm not saying you'll often want to use it, just that finally you might ever want to use it. It's not good, but it's not completely useless. You might use it to shoot down an abductor or harvester early in the game, or a supply ship in the later game. And as before, you can still use it to ensure the small scout makes it safely to the ground.
The larger alien craft are quicker to run away now. Usually you still won't notice anything different, but if you take too long to shoot them down, even the biggest ones might flee. I noticed it especially when using Firestorms equipped with laser beams to attack abductors. The abductor can go slightly faster, thus is able to flee combat from a Firestorm. I had mine equipped with a laser beam and plasma autocannon, and any ship I could out-range I was saving my ammo and beating them slow. After enough abductors ran away, I learned it's best to spend the elerium to shoot them down faster.
More details in the OP.