I am a huge fan of the chaotic nature of the battles and architecture of the first part of the game. It seems unscripted, and I like the cramped style of combat. It prevents the ridiculous "Run in circles around the enemies and let them kill each other" technique, which is common in large battles.
I ended up taking the timeline where you get infected, and I was having a good time with those levels, though they are somewhat less fun than the ones where you cooperate with humans. I got stuck on the lava level Jjaro Jjaro Revolution. I ran through it about 30 times, getting farther each time, but I lost hope after a while. It's just way to hard, and minutes of focused killing can be obliterated because you just got knocked off into the lava. I'm okay with long stretches without a save terminal, but that was too long.
So to summarize, the first few levels were amazingly refreshing, and reminded me how I used to feel playing the original games oh so many years ago. It loses that charm towards the middle of the game, though continues to be very good.
This scenario has amazingly designed levels. They are the main reason I stuck it through to the end. There is some beautiful architecture in this map set, the lava level (forgot the title) comes to mind. The combat is very hard, and you basically have to save after every encounter. One problem is the massive over use of red defenders. They are not quite as much fun to fight as their ubiquity would suggest. The weapons are generally impotent, which you get used to after a bit. The energy katar invincibility totally changes the gameplay once it comes out. It's a nice addition and makes the following levels more manageable, though makes the final boss battle somewhat trivial. Finally, the terminal texts are boring. I stopped reading them after about the 2nd level.
The skulls were a fun touch. I managed to get 31 at the end.
All in all a great scenario, very solid. Could use a rewriting of the terminals, and perhaps a reduction of the amount of red defenders.