I would like to see a fundamental change in the way we siege and take over enemy planets, or even neutral planets.

Each planet could have random number of native people living on them, neutral to every empire. Some planets would have no one on them.  Your empire's colony ship will create a colony on a empty planet to same way that the game currently works. But you can't simply colonize a neutral planet with existing people. Each occupied planet has a loyalty meter. You can either persuade them to your side peacefully through culture or kindness.  Friendly Culture causes increased loyalty over time. Buying planetary upgrades cause increased loyalty. Destroying enemy garrisons holding a planet hostage will increase loyalty to your side.

Well, if none of that works. you can just glass the planet's surface and start fresh. This means rebuilding everything from scratch. It would generally be extremely expensive to recreate a huge megapolis city planet from a barren wasteland, but possible. This leads to the next suggestions, military ways to take a planet without destroying everything.  You can control a planet whom is loyal to another empire by using ground forces garrisoned to maintain control. The higher number of garrisons lead to a more stable planet, kept in line by force. The opposing empire only has to destroy the garrison and loyalty will flip the planet's ownership back to empire the planet is loyal to, if that is no one, it will go neutral again.

The question is how to get the garrisons onto the planet to begin with, and how to defend against them. Every capital ship will have capacity to carry one garrison unit. The capital ship can choose to launch shuttles to the planets surface to try and take control. the more loyalty you have, the less garrisons needed to keep the planet stable. If the planet becomes unstable, production goes down as civilians riot and fight each other. More garrisons are needed to maintain peaceand stability, Or other peaceful measures are needed to raise loyalty. Once a garrison is used up, it is replenished by having your capital ship visit a world you own that you control by loyalty, not through military garrisons.  To prevent enemy ships from sending their garrisons, you must build planetary shield emitters in orbit. shuttles cannot penetrate the shield, the shield must be destroyed first.

If an empire sends a garrison to a planet that has a garrison from the enemy empire, the outcome goes like this.

Attacking with 5 invasion garrisons against 1 defending garrisons. the defenders gain 1 point advantage. and whomever the planet is most loyalty to gain a 2 point advantage. So if the defenders have the loyalty of the citizens, defender score is 1+1+2=4 so attackers win with 1 surviving garrison. If they had attacked with 4 garrions, all 4 would have been wiped out and the single defender would also have been destroyed. If they had attacked with 3, all 3 would be destroyed, and the single defender survived, because the bonus points are counted first. That means that a planet controled by a military garrison, but which is loyal to the enemy empire can be retaken by a single invasion garrison. 1garrison+2loyalty bonus=3 attack vs 1garrison+1defense bonus=2 defense

Of course there can be many many defensive garrisons which make attacking by invasion very difficult with a defending fleet. The shuttles, once launched, are targetable by orbital defenses and can be thinned out before ground engagement even begins.  There is a maximum of 1 garrison per planet per capital ship you own. That means if you had capacity for 3 capital ships, you can only have a maximum of 3 defensive garrisons per planet.  And high population terran worlds which are not loyal to your empire can take maybe 10 defensive garrisons to keep it stable.

Planetary bombardment lowers loyalty of the target planet. If you just give up on trying to take the planet with an invasion, you can use siege frigates or your capitals to bomb the planet's surface, this will destroy enemy garrisons, but almost surely cause a sharp increase in the loyalty to the enemy empire.  Once all garrisons are destroyed, any continued bombardment will start to destroy civilians, infrastructure, logistics and tactical slots. You can still fully destroy the planet and recolonize it fresh, but it may end up costing more money to fully rebuild it. A fresh new colony on an empty planet has 100% loyalty to its empire, the same rules apply to them as well, the loyalty can decrease.

So if an enemy homeworld is 100% loyal their side, then using planetary bombardment to take out their garrisons does nothing to hurt your loyalty meter, since its already maxed out against you. Once enemy garrisons are cleared out, you can proceed to invade with your own, or just continue destroying the whole planet to start fresh. It will probably be more profitable to take it intact and try to raise its loyalty. A fully maxed out planet can not be easily swayed to your side, since all of its upgrades are already aquired, so the only method is to wait for your culture to very slowly raise it up. This makes it ripe for a counter takeover which can easily succeed. If there aren't enough garrisons.

Friendly Culture slowly raises loyalty of a planet, it will eventually cause neutral planets to flip to your empire without ever even going there. Enemy culture likewise will cause a drop, and require more garrisons to maintain control, and make a hostile take over much easier.

I had a bunch of ideas there that mostly work in an interlocking way. The main point is to decide when to take over a planet, either hostile or peaceful. Or destroy it and start over, at the tremendous cost or rebuilding everything. If you take control of a massive world, you gain the immediate tax income, all planetary upgrades already purchased.

More ideas, Starbases aux government upgrade can make a planet immune to peacful loyalty flipping without military action. And a starbase's presense alone cause a bonus to planet loyalty that is gained over time.