[sachmo]

The ability to target facilities, cargo, or population would be nice. There have been times that I wanted to destroy a shipyard in my initial attack, but my bombardment winds up killing one WP, a couple of million pop, and a research lab. If you added an inherent defense for these facilities, it would require a player to use a bit more strategy when attacking a planet.
Also, how about not only planetary shields, but also facilities that would protect your population, facilities, or weapons platforms?
1. Bunkers (or shelters)- would add a defense value to your population. Effect would be cumlative.
2. Hardened defense bases-would increase defense value of weapons platforms
3. Hardened Facilities-possibly an upgrade? Would increase the cost of a facility but add a defense factor for the facilities.

I don't think any of these would unbalance the game. It would require the planet owning player to sacrifice space/resources to create a defensive planet. Also, it would take a lot longer for a fleet to destroy a world.

If you added some other things like beam weapons damage being decreased by atmosphere (thanks MOO!) or increase planetary weapons range, maybe it would make planetary attacks more interesting.