But! You don't need to put everything in the same system. You don't need to have a free port on every colony. You don't need multiple high commands, or even any. You don't need commerce. All I can really tell you is I've seen plenty of "I can't make any money from colonies because of the hostile activity system" savegames and it was pretty much always something that could be resolved in zero in-game days by just adjusting some immediate colony settings. I remember one that went from being negative to being something like 200k+ credits a month.
The good news is this doesn't really matter anymore, since the penalties are going anyway 
Yes, but it's a management issue.
You either have to kill the large late game expedition fleets yourself, or you have to have one very expensive high command with a cryoarithmetic engine, or multiple cheaper high commands. If you go the route of letting your system fleets handle it, it has to be all within one system. Or you'll just have to personally defend your other systems.
The high command(s) typically get supported by one very profitable colony, usually a habitable world. If the player gets unlucky, and only has the option of a very high hazard system, and doesn't find a dealmaker holosuite, then it becomes a requirement for that colony to also have free port enabled, which can make it very fragile.
I'm glad it won't be an issue anymore, I was just trying to explain there were actual circumstances that required players to keep HA low.
Yeah, I'm well aware! I thought the tone in the blog post conveyed that I was joking around a bit, too. In othr words, the implementation of that particular crisis is a bit of a meme, too.
Sorry about that then, it's always difficult to tell when people are joking online. Still, I recommend keeping the idea of Remnants raiding from other nearby star system in the back of your mind.
There's already a story precedent for them to occasionally find their way to other star systems.
As you noted, you can't actually wipe them out. And the event that attacks the player is literally easier to deal with - and suppress the threat for the rest of the playthrough - then going around decivilizing Pather worlds. So I'm not sure that makes a ton of sense.
You can with Nex. Which is the issue. While I don't know how it will be fully implemented, them being able to destroy the player's worlds over mining, refining, and a fullerene spool, is a bridge too far. It will start pushing the game in the direction where Nexerelin is recommended for new players to start with, and old players feel it's required to fix this issue. IE towards that Bethesda style path where modders do what they can to fix issues or annoyances with the game that shouldn't have been there at all.
Either all plans for invasion and saturation bombings need to be dialed back, the player needs a method of ensuring they can't happen to begin with, or the player needs a functional method of reprisals.
I don't understand why you seem to want the player to have immortal enemies that can severely harm the player, that the player can't harm or permanently end.
As for how long it takes to deal with them. It's a couple gas tanks of fuel, and a couple rounds of combat with stations. That's pretty quick when compared to possibly dealing with a sat bomb when you're at the opposite end of the sector and can't return to your colony in time, or "managing" their attacks from when you start a colony to when you quit playing.
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I think you're making some wrong assumptions (which, fair enough, you don't have full info) and then extrapolating from them with a little too much vigor and then *also* assuming everyone is going to play the same way that you do. I kind of get where you're coming from, I just think most of what you've said there is way, way, way too extreme, to the point where imo it's mostly inapplicable
I mean, maybe "if they sent a semi-hostile fleet to my system, I will escalate to saturation bombardments immediately" is true for you - and for a few other players - but that kind of approach is not something I'm going to design around. You can certainly *do* that! But the game isn't going to be built around that hair-trigger attitude, if that makes sense.
(Edit: for one, that makes for a less believable world. And regardless, sat-bombardment is basically an option the game assumes the player doesn't have. It's something you can do, sure. But if you have done it, in my mind the game's gone off the rails enough that it basically doesn't matter how it pans out.)
(You can also avoid most of these crises by not doing certain things, same as the Hegemony one. Not that I'd particularly recommend it.)
I will admit I have an extreme hair trigger for trespassers, but everything else is equal force. If the Sindrian Diktat turns to sat bombing I will destroy Sindria alone. The same holds true for the League's military worlds. The only reason for my particular spite towards the Luddics is their cooperative nature and the combination of an invasion and sat bombing coming from them.
Getting attacked by Pathers in Church territory, and watching an independent fleet get killed by a Church station that was assisting a Pather, also has not done anything positive towards my opinion of them.
As for other players, they'll try to play by the rules and not go down the route of wiping out a third of the sector, but annoyance and frustration will eventually win out.
As for sat-bombing not being "cannon" then perhaps it should be removed entirely, for both player and NPC factions. Otherwise if the LP and possibly the SD is going to use it against the player as a "solution" to their problems, then it needs to be a solution for the player's problems. Which means story protection needs to be removed with a warning, and LP needs to cease to exist if all their planets and stations are destroyed. Otherwise Nexerelin, a mod, becomes the solution to this issue which I'm sure you don't want.
As long as all things to be avoided are reasonable and possible, it's fine. It's also fine if the player can't do all of them at once, as in the player has to choose which lines to cross knowing they will end up fighting those factions. If it's a line like don't produce fuel, then it's not going to be fine.