I'm a fan of Master of Orion II as well. In my opinion, it is the best space strategy game ever created and probably that ever will be created. It was released in 1996 and I've been waiting ever since for a worthy successor to MOO, but so far, many excellent games have fallen short.
For those of you unfamiliar with the game, I'll try to list a few of the features that made it special.
Ships had hull, shield, armor, engines, weapons, sensors, and personell. There were weapons specialized to damage each of these. For example, ion weapons to drop thier shields, gyro destabilizers to damage the hull, neutron beams to kill the personell, etc. The ships had upgrades to counter them, such as reinforced hull to counter gyro destabilizers, extra shields, extra armor, etc. This created tactical variety as you tried to design your ships to counter your opponent's ships.
Shields had four facings. When a shield became weak or went down, you could rotate your ship to try to keep the weak shield away from your enemy. This added to the tactics during a fight.
Planets had missile bases, star bases, fighter squadrons, and planetary beam weapons defending them. Attacking a planet with a fleet had a lot of interesting tactics dealing with all of these.
If you took down an opponent's shield, you could beam your marines over and have them try to destroy particular systems, such as the engines or weapons.
You could equip your ships with assault shuttles and send them to board the starbases, destroying systems or even taking them over completely.
There was a huge variety of special systems you could research and add to your ships such as black hole generators, teleporters, etc. You could design your ships, allocating weapons, engines, defensive systems, etc.
Ships could be equipped with point defense. They would shoot down incoming missiles. They would shoot down incoming missiles heading towards other ships in your fleet if they were close enough. When closing on a planet, one of the things I did was use a formation that maximized point defense.
Instead of bombing planets into oblivion, you could send in the marines and take it over. Then you had to manage the happiness of the local population. The different races had different special abilities. You kept the special abilities of the population on the planet.
The best planets were defended by bosses. You could steal technology. You could use spies to incite rebellion or knock out critical planetary defenses prior to invasion.
These are just a few of the features of Master of Orion II. It put all of this together in comprehensive way that has yet to be matched. I hope that someday, a developer will make another game like it only with updated graphics. Most of those things are beyond the realm of modding though.