It's a great game, certainly the game of it's genre I enjoyed the most. I'm with Ace, the ship design is hands down the best I've seen in 4x game. Lots of interesting stuff you could do with your ships.
It was, however, not the best balanced game in the world. Creative was way too valuable, and in general it was a game of he with the highest tech wins. It had little annoyances too - like not being able to decide how your starbases were equipped (I'd much much rather have star fortresses armed with autofire disruptors or plasma cannons then death rays.) Then you had the whole phasing cloak + time warp facilitator + hyper X capacitors thing, where ships became near invincible. I was often annoyed that there wasn't any planetary expansion tech - if you wanted to make your tiny world into a large world, you had to give it to another race, turn a stellar convertor on it, then have another colony in the same system put it back together. Same deal with toxic worlds.
And you know, I never even noticed the command point system. Typically I either had no fleet worth speaking of, or a small number of technologically superior ships, or I had income so off the charts I could pretty much ignore the penalty from command points.