Here's how I see "Strategic Bombing" planet attack cycle working:
STEP 1) You move your fleet onto a planet.
a) Expend one movement point.

If there are no defenders in orbit, go to step 3;
c) Otherwise, dialogue box comes up: "Do you wish to attack the planet itself, or just the defending fleet?
d) If answer is planet, got to step 4, else, go to step 2;
STEP 2) Conduct a regular battle between the attacking fleet and all ships in orbit, which are treated as a single fleet (bonus for being close to a planet). When the battle is over, any remaining attacking ships are kicked back to the square where they started. END CYCLE.
[Allows defending ships to do more than use up the enemy's movement points, but they have to come out from under the planet's guns to do it]
Step 3) a) If there are no troop transports in the attacking force, go to step 4.

Otherwise, pop up dialogue box "do you wish to invade?"
c) If the answer is no, go to step 4;
d) If the planet has no active Defense Grids, go directly to the standard invasion routine, END CYCLE.
e) Otherwise, fight a battle between the attacking fleet and the planet, with damage scored by the attacker applied to the planet's active defense grids. For each X number of rounds (see below), one troop transport (determined randomly) is considered to have landed, and is removed from the attacking fleet. When all transports are destroyed or landed, the battle ends. If transports succeeded in landing, fight a regular ground battle using the troops from the transports that made it through. END CYCLE.
[Means that there will be impetus to have shielded "combat" transports, and you can still have a "combat landing" on a heavily defended world]
STEP 4) Pop up a window showing all the buildings on the planet, with level of detail dependent on the race's intel (minimally, all you could see would be generic symbols for "morale building," "research building", etc.). Attacker selects one Target Building as his target. Go to step 5.
STEP 5) Conduct a battle between the attacking fleet and all defenders as a fleet (if any) AND the planet. The planet uses the combined attack value form all Defense Grids (if any, see below), and is treated as just another ship. However, damage it takes is applied to the Target Building. Combat ends when the Target Building is destroyed, or when a X combat rounds is reached (see below). END CYCLE.
[Allows you to attack particular buildings from space, but you play into the defender's hands... he gets to use his fleet, and his planet's guns]
NOTES AND SUCH:
X ROUNDS: The set number of rounds (X above) would have to be playtested to see what works best (five or ten, maybe). In game terms, it has to do with "the mechanics of fighting close to a large planetary body." Yeah, right. Basically it is intended to give the attacker a break, in case their force is getting slaughtered, and to prevent a strong fleet with lots of movement points from levelling an entire world in one turn.
BUILDINGS: Would have a set number of hit points (100?) Damage would basically set them back in terms of production... A building that lost 10% of its hit points would be considered under construction, and 90% complete. However, you would not be allowed to spend more money now to finish it (the debris has to be cleared, your construction crews have to get there, etc., only elbow grease can do the job).
[This means a building would be useless if even slightly damaged. It has to be, otherwise, attacking a high-quality world would do no good... if it makes 125 shields, who cares if that drops to 123?]
DEFENSE GRID: Unlike other buildings, these buildings actually DO still function when damaged, because they represent a network of separate installations rather than just one. for each 10% of their hit points they take, they lose a 10% chunk of certain capabilities.
There would be two "defense grid" buildings, Passive and Active. "Passive" buildings would ADD a set amount of defense value to every non-defense grid building, say 10 Planetary Defense points(that is, 10 points, regardless of whether the attack is missile, gun, or beam). This value would drop as the building took damage. The building itself would have a Planetary Defense of 10, which would not drop with damage (it represents the armor around the interceptor missile silos or whatever).
[Planetary Defense is a mix of the three standard defensive technologies, as well as a few special ones like magnetic field manipulation, atmospheric distortion, big thick piles of rock for armor, and camoflage. It is also a way to avoid having three different types of passive defense building!]
"Active" buildings would have their own Planetary Defense value, say 10, but this would not go down with damage (every flak battery has the same degree of protection). There would be different types: gun, beam, and missile. Each building would have ten weapons (actually, ten buildings with one each), of the best of that type you have available (ten lasers, ten plasmas, Ten Harpoons, etc.). These could be upgraded as you get better weapons.
Additional Defense Grid techs would allow you to build DG buildings with higher Planetary Defense values, and defensive buildings that add a greater amount of Planetary Defense to other buildings. You could also have a Tech that added mroe hitpoints to buildings.