I felt that the option of orbital bombardment was missing from GC. It would be a good idea to implement new class of ship - orbital bomber. Then you would have different options such as nuclear/ neutron/ biological/ anti-matter orbital strikes.
The consequences would differ from one option to another. There will be temporary reductions in population and economic output, population and economy growth rates and destruction of special buildings. Bomber ships would be more slow then normal ships but will be faster then transports. The tactic of their use will be similar to transports: destroy orbital defence of an opponent then sneak one bomber and bomb his planet.