I think Orbital defenses should be handled like regular fleet engagements.
Here's my reasoning: as far as the Imperium battle tactics go, you cannot bombard a planet with an active orbital defense grid. Bombardment takes hours and hours of sustained fire to be truly effective, something you can't do when you're getting hammered by cruiser-class weapons mounted on defense platforms. You have to be geo stationary orbit for many type of bombardment weapons to work, as well.
So, in my mind, you'd have to deal with orbital weapons platforms on the same level as fleets.
That doesn't address ground-based torpedo silos and what not though. Not quite sure how you handle that in the current flow of the game. I suppose they could just passively whittle away at hull strength every turn an enemy fleet is in orbit, until they're bombarded. (Ground defenses generally being the first thing targeted in an orbital bombardment.) Thing is though, those ground-based defenses are like, hab-block sized torpedoes capable of one-shotting a strike cruiser. To do them justice they can't just be an annoyance. But given that orbit-ground combat doesn't really exist in the game conceptually, I'm not sure how you address them. Because there's no way I want to put fleets in orbit, loaded company strength, if there's a % chance they're just going to get vaporized when I click End Turn.
Slightly different but related topic, you should not be able to land troops on a planet that has hostile ships in orbit (or orbital defense platforms if they ever make it in.) Nor should you be able to leave orbit with the same. Reason being is ships will interdict any attempts to drop ground troops, and once you get into system they'll attack you while you're plotting a warp jump to leave.
There should be an exception for hot dropping troops onto a planet with a hostile fleet in orbit. Happens all the time in fluff. Ships will plow through a defensive line in orbit to drop troops to the surface, almost always at the cost of the ship in question. I imagine when you move a ship into orbit with a hostile fleet, the "Attack" button would change to "Punch through Blockade", and if successful, woud unload all the troops on your ships to the planet before immediately gong to the fleet combat screen.
One other point about orbital maneuvers. They're a bit incomplete based on how the game structures itself. When a ship exists the warp into a system, it typically does it far away them, like a week's travel, because to jump into or out of the active gravity well of a planet or star is to invite disaster during warp translation. Tearing apart of ships and planets, and so forth. (In 40k lore, this point is known as the Mendeville point, or the point at which it is or is not safe to translate to the Warp.)
The game
kinda models us being in the outer reaches of the system by letting us choose what planet to interact with. But fleets are generally considered to be in the system at large instead of at a planet.
So. What if "System" was it's own actual place of space, and fleets were either "in system" or "at planet." It would take one turn to go from "in system" to "at planet" and one turn to go from "at planet" to "at planet."
I think this would be good for the game for several reasons:
1. It more accurate reflects fleet movement fluff-style.
2. It would increase the amount of time exploration takes.
3. It would allow people to bypass hostile systems while (with what I said above about not being able to land or bombard planets with hostile fleets at them) forcing them to address enemy fleets on a planetary basis instead of a system-wide basis all the time.
4. It would allow for more interesting fleet-based scenarios. So for example, instead of facing a unified ork fleet of 10 rocks or whatever in a system, at the planetary level that fleet might be spread out over several planets. Systems would be threatened faster than the current method, which seems like one planet at a time falls before the next gets attacked. You might end up chasing fleets, coming to their rescue, putting all your eggs in one basket at the best hive world of the system....
In terms of UI changes the game would need to address, the star map I don't think would need to change at all. You'd see a fleet group at the system level, letting you know, yes, there's a fleet present somewhere in teh system.
The planetary view would need to change fairly substantially. It'd basically need to be able to display fleet icons around the planets, and have an "in system" section to display what fleets are just sort of floating around. You'd need to be able to divide and assign parts of a fleet to different planets, so basically the system-level ship selector present on the planetary view. The whole logic about what you've got selected interacting with what planet would have to change, since each ship at a planet or in system would be considered in a separate, exclusive area.
There'd be some complications, namely, the AI knowing how to juggle its fleet being spread out, and how to control for being "in system" or "at planet" when you're trying to order the fleet to move from the system view. I suppose the the fleet selection menu could grey out ships in the fleet that are "at planet", telling the player that they cannot be part of the warp jump until they move to "in system."
So basically, instead of clicking on a planet in star map and getting a popup-style view of the system, in this, clicking on a planet would take you to the "system view, and clicking on a planet would bring up the planet view as normal.
That's a lot to take in, but man, I really think the game could use another layer like that. Here, have a crappy GIMP picture of how I see this: