As a practical matter you cannot make a 4X game that does not make ships supreme.
If it were possible to fortify a planet so that it could not be taken by a fleet of ships you would have a game that would frequently get into stalemates. So, the starship is the ultimate weapon in SE just as in any other 4X game.
That said, the best way to defend a planet is, like most things in SE, with a combined strategy. WPs on the planet with direct-fire weapons using mounts (assuming you have a mod that uses these for WPs) and satellites with missiles and PDC. This is important. The satellites with PDC defend your planet against missile attack and can launch long-range counter-attacks with their own missiles. Since sats cannot be targetted by missiles your enemy would have to approach the planet to attack them directly and then the heavy weapons on the planet can fire on them. This is a fairly deadly combination. But, as with anything you can be overwhelmed by sheer numbers or a large technological advantage.
A fleet of ships is also effective, of course. But since ships cost maintenance it's usually not possible to have a fleet over every planet or even in every system.
There are also mines of course. Without a doubt mines are the cheapest and most effective defense. That's why I hate them. They are too simplistic. They ALWAYS hit, and there's no defense but a generic "mine sweeper" that also ALWAYS works. It's just disappointing that a game as sophisticated as SE would still be so crude aboutmines.
[This message has been edited by Baron Munchausen (edited 04 September 2001).]