Also: the Lair power. Oh, but of course
I don't like the random mission generator. It reminds me too much of a video game random encounter thing. Seems like just a way to work in a bit of space between big story elements. The missions are too generic as well. I can see doing a few of them just as filler, but without the interesting backplots and stuff of the pre-made ones, they are just too boring. A gunfight is just a gunfight at the end of the day, unless the players care about the results.
It's not really a problem - players don't tend to have total freedom in our games anyway. NE has about the same level of freedom we usually have - the GM decides that something happens, and the players respond in their own (insane) fashion. I'd probably just, every so often, ask the players if there is anything they are doing downtime. I imagine that they will want to snoop around the bar of that guy whose neutrality is mentioned, just to check it out. The problem being to prevent that sort of thing taking over entire sessions.
The story is really good though. The feel of it is all good as well - lots of secret lairs with diabolical equipment just waiting to be plundered, and plenty of opportunity to throw cars (with inhabitants still inside, of course) at various alien vehicles
And I like how you can make it a really long campaign, by inserting more missions and giving less exp per session, or making it a short campaign, using just the core missions and a few extras, and giving a lot of exp reward. Though knowing my group, it'll take a session to do the short missions, and 2 for the long ones. We tend to have too many diversions and OOC discussions for that.