Ok, I think I misread your post. I see what you mean now.
This could be mostly done now with changes to the settings.txt file.
Raise the damage to kill one pop, leave the standard weapons alone and raise the damage of the exsisting planetary weapons. No need for special abilities.
Raise the defending units per population, and hit points and attack strength. No need for actual special units. Just make the exsisting militia a little tougher.
With these changes it would be harder to glass a planet, and it would take more troops to conquer one. The weapon platforms would get toasted fairly early in the battle if the attacker was using planetary weapons, but that's not nessecarily a bad thing. You don't want planets to be inpenatrable fortresses, just harder to glass.
On a side note you could come up with some neat weapon platform only weapons. Missles that fire every 15 turns, but can hit anything on the combat map. Direct fire beams that can reach way out and touch you.
The result of these changes would be... If you
want to glass a planet, you'd have to use planetary weaposns, or have a
lot of standard weapon ships. You could make the planetary weapon components as expensive as you want to limit there use.
If you want to conquer a world you need more troops than you do now, and you'd have a lot of losses among you troops. No more conquering 8 systems with one small transport and 200 troops.
Put them in a fleet with some standard weapons to eliminate any pesky weapon platforms and then drop troops. Since the damage to kill one pop would be higher, you wouldn't have as much wash over damage and the planet would be more or less intact if the troops succeed in the assault.
Does anyone know how the game calculates whether a facilitiy gets popped? It appears to be a ratio of population killed, but I can't figure it out exactly.
Geoschmo