Like the easy encounter generation (haven't actually read about it in the book yet), but I am a tad bit worried that the bare-bones minimum and on-the-spot encounter generation will leave me struggling to improvise entertaining scenarios and interesting aliens.
Do not worry at all. Just play the game following the book and you'll be fine. There is an example of a planet in there (Goya, populated by Dinosaurs) and it has ideas on what a GM
might have in mind. It also tells the GM to hold the ideas lightly, though, since play might take the game in a different direction.
How would you describe Dinosaurs in any role-playing game? D&D, say? However you think they would act and react then describe them as doing that. As GM you will have your Alien Ability to roll against and the results of the dice rolls will tell you how successful or not the dinosaurs and the Troopers are.
This is not some "GM showz l33t Improv Skillz to impress the players" thing. It's an RPG where the GM plays the aliens and NPC troopers, while the players play their PCs (one of whom will be in charge of the squad). I think there is some pretty good advice about how to actually role-play too in the book. And the GM advice really helps too.
I wasn't aware that the token system for a set number of encounters was supposed to be kept secret to the players. Is this the norm or just one way of playing it?
For your first mission (to help you learn the rules) I advise planning out a set number of encounters and for the GM to allocate a set number of Threat Tokens to them. Once you've done that and played it through, you'll then understand how Threat Tokens work and will have formed an opinion on how best to use them. From them on allocate them to encounters how you wish.
I always keep the overall pile openly on the table. It's a wonderful pacing mechanic so that the GM and players can see how far they are through the mission. If the players nibble around the edges of the enemy then I do what the book advises and push only a Threat Token or two into the next encounter - a small skirmish. If the players rush headlong into the heart of the enemy I throw in more Threat Tokens to the encounter. When they're all done then the planet is over and we do "Between Missions" stuff and move on to the next planet.
If you're stuck for inspiring planet ideas I think the best mine is the list of Actual Plays on the
homepage.
Hope this helps. Crack out the beers and play.