I was also impressed by the siren lights and the landscape feature for an M1 scenario. I've just read the Trojan Manual, as Steve requested here :), and it sure sounds like they spent a bunch of sleepless months getting this thing sorted!
I've also just played Prelude again, and, wouldn't you know it, after not having thought about it until just reading here about the Bobs getting killed in the doors, I got killed in one myself, due to a Bob standing in the way :/.
I'm a bit confused with the timing - the manual talks about the battle against the Pfhor with the Humans and the S'pht'kr, or something like that, but this wasn't known until the end of M2, I thought. Was that particular bit of the manual updated after the M2/Win release of the scenario or something?
And just one more thing - Arrival contains a switch and platform puzzle. Such a thing as would have been commonplace when M1 was the only comparison, but which have been rare since. I found it quite fun, which was not something I used to describe the M1 Defend THIS! puzzles.
Other than that, I found the wait for only a 1x recharger was rather long, given that we're just learning about these weapons and these aliens. Also probably the fact that I'm playing on TC didn't help :).