Ok, first I wanted this post to be simply about having the option of destroying a planet with my fleet. Instead I think I will discuss it and a few other ideas on how to deal with enemy planets.
1. Total destruction of a planet - This one is pretty self explanitory. On larger maps I get tired of having to send troop transports to get rid of my enemies... frankly when you are dealing with hundreds of planets, the amount of transports and troops you need is just mind boggling. The way this technique would work would add a option for your fleet when they attack a planet to destroy it. If they had enough fire power, or the right technology, they could simply obliterate the planet and everything on it. The effect could be similar to the random event that turns a planet into an asteroid field.
2. Extermination squads - Again brought about by my annoyance of killing off hundreds of worlds. I'm tired of having to build 1 transport and disposable army to take over each planet. What this would allow you to do is create a troop transport and army that could be re-used. It would act just like a normal land battle except after the fight is over (and hopefully you won), the colony is totally destroyed and the remaining forces are loaded back into your transports to be moved to another planet.
3. Planetary bombardment - Tired of having your fleet just sit idle over an enemy planet because they can't do anything to it? Well with this they could, it would work similar to the total destruction proposed in number one, but would simply demolish the planet to the point of uselessness. Gives you another option to skip having to bring along a troop transport.