This game is one of those non-collectible CCG's, I'm not sure what the right term is. It comes with decks for a couple of empires, all ready for you to have a space battle between different space empires.
This game cleverly tries to avoid some of the pitfalls of CCG's like Magic: The Gathering (my favorite CCG). In particular, the extreme randomness that can cause many games to be lopsided one way or the other. Here, instead of drawing forces randomly, you purchase your starting spaceships, and the cards merely improve the capabilities of those spaceships. You can't be "mana-hosed" because you get a fixed number of command points per turn, and even without improvement it is enough to buy any one card. Also, you can discard and redraw every card you don't use every turn, so you go through a lot of cards and are never stuck with anything you don't want. This is a much more controlled, balanced game than MTG (even assuming you play MTG, as I do, with decks that are equally good against each other on average). And the actual game balance of the individual cards seems to be much better than I'm used to; it looks like I'd have to play it more to figure out whether anything is off with the balance. In terms of technique with the individual game mechanics, this is my kind of game.
My only real issue is not with any specifics, but with the overall fun factor of the game. To me, the fun part of MTG is in drawing a random selection of forces and abilities, and having to make the best battle strategy you can from what you draw. The game wouldn't be that interesting if you pre-selected the cards, as the actual game mechanics are fairly primitive. With Flagship, that core randomness is greatly minimized. It seems like the cards just add spice and extra variability to the space combat game between your preselected ships. The problem is that the basic space combat game is completely uninteresting without the cards, so the cards have a very difficult task trying to make up for that. It feels like it would be cool if more were going on in the base game, maybe the ships were maneuvering around on a map and shooting each other with dice rolls, and the cards were adding on top of that. As it is, I feel a little bit like I am playing not so much a game, as a nicely designed simulation of a game, a way to determine who would win in a battle between the Standing Nations and the Kirkin Swarm. Sort of like when I used to take a bunch of RPG characters and have them roll attacks against each other without using the map, to see who would win. Only here, the randomness of what you draw each turn from the deck is used as a substitute for the randomness of dice rolls.