A bunch of ideas....
1) Cloaking ships/Anti-Cloaking ships (cloakers visible when attacking another ship only)
1a) This could work for structures too, I guess. Maybe a logistics structure could hide/cloak the fleet defending your planet, or conversely uncloak a cloaked ship that entered the warp well.
1b) An alternative to cloaking could be a Chameleon Device that could emulate an enemy ship type to facilitate a spy mission, or surprise attack.
2) Spy on adjacent enemy (or allied) planets. I'm thinking that there would be some sort of cost associated with the spy attempt, with only a certain chance of success. Upon failure, the planet owner could possibly be notified. Other information gained from a successful spy attempt (could be categorized and selectable) could be general fleet, economic, or empire (planets owned, etc.) information, and the list goes on.
2a) Sabotage comes to mind here too. Maybe if you could successfully send in a spy to disable defensive structures before launching an attack.
3) Worm Hole like travel to another point in your empire. In VGA Planets, this was also a ship ability called Chunneling. Basically a way to get your ships to another point in space without having to physically travel there. Would help if portions of your empire got disconnected, or if your empire was very large. Obviously, the cost of something like this would be high, but would add a lot of strategic options. Could also be a racial ability.
4) Ability to trade/sell technology, among other things (similar to GalCiv)
5) Space phenomena, like ION storms - would disrupt jumps between worlds, or even knock out defenses, or disrupt shields, etc. for a period of time.
6) Some sort of alternative to direct planetary assault (beside cultural influence), like gas bombing/irradiating the population, or landing a war party to capture the planet with its defenses intact (logistics/defensive structures would become yours afterward). This would also save you the time of having to blow all of those things away.
7) Advanced refinery ships/structures that could make Crystal and Metal over a period of time.
8) Self-Destruct mechanism that would damage surrounding ships/structures (including your own).
9) Native life on planets that could enhance, or hinder aspects of colonization, economy, logistics, etc.
10) A super tractor beam that could pull ships within range of Guass guns.
*) Another general question that I have is, and maybe I just didn't look for this hard enough, how do I find out what the capital ship abilities are? Some of the ship descriptions are fairly general. I would like to see some doc on what some of the support ships actually do (this actually goes for any ship that has support capabilities). Better yet, have short descriptions added to ship info screen when the ship is moused over. Could add an interface option to turn on verbose detail on ship descriptions.
**) One last thing...how about being able to choose my own install directory for the game, and/or Stardock for that matter. I think that you are currently restricted to only your Program files directory.
although the latter doesnt have anything to do with the topic, i did add a bit in it about self-destruct damage.
Actually, planetary defense overhaul has its own thread, or three, that you should post in. Most people tend to aggree that the gauss gun needs tweaking to be more effective, but its general role (close in defense) is exactly what it needs to be. Hangars (and a few other ideas) were thrown around as "grav well control" devices, while gauss cannons were effectively just point defense systems (defend a given point in the grav well).

