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[Megas]

You have to remember that once the game stops trying to beat us, it gets boring fast.  Successful colonies can easily negate a vast majority of the challenges the game throws at us, so colony-specific problems keep things from getting stale.

I'd prefer stale to actively annoying though. I'd assume most folk would as well?

I prefer boring to babysitting.  I avoid AI cores for colonies like the plague (usually), and I do not allow Pather interest to exceed +6 on a size 4+ world.  I may have about a little over half income of fully min-maxed colonies, but I still have enough income (provided I do not Restore every ship I collect).  I simply do not want spam telephone calls alerts interrupting whatever I am doing, especially if it is time-sensitive (and rushing to defend my home means failing the mission or quest I was working on and/or traveling half the sector or more through hyperspace to reach home).

I have attempted to stop all expeditions by destroying all of the core worlds once.  It did not work because pirates kept harassing me (back in a release when pirate raids had no delay for respawning.)  But I am willing to nuke core worlds off the map (and lose income) if it means I can eliminate the babysitting.  (At the very least, I can nuke H off the map then buildup my size 3 world collection to make up for lost income.)

[Aeson]

It's rare I actually colonize Penelope, as it is usually a terrible system.

Really? In my experience, Penelope's Star is usually a decent to good system - it has great accessibility by default; it's fairly likely to have decent sources of Ore, Rare Ore, and Volatiles since it's guaranteed to have a volcanic planet, a cryovolcanic planet, and two gas giants; it has three of the best airless rocks in the game for setting up Refining and Fuel Production, especially if you don't want to settle in a system already colonized by a major faction; it pretty much always has at least one decent or better site for any colony item other than Soil Nanites; and a number of the potential colonies will always be close to one another due to being planet/moon groups and thus are relatively convenient to visit or defend. About the only real downsides I can think of for Penelope's Star are that it doesn't usually have arable land or organics, is rarely within range of a hypershunt, and doesn't have a gate, and those aren't very significant downsides.

Also, with nine guaranteed planets and moons, including one Very Hot and three Hot, it's one of the best places to set up if you want to make extensive use of AI cores on your colonies and don't want to be constantly running back to deal with AI inspections - very few systems have greater, or even equivalent, potential for military infrastructure.

[eert5rty7u8i9i7u6yrewqdef]

It's rare I actually colonize Penelope, as it is usually a terrible system.

Really? In my experience, Penelope's Star is usually a decent to good system - it has great accessibility by default; it's fairly likely to have decent sources of Ore, Rare Ore, and Volatiles since it's guaranteed to have a volcanic planet, a cryovolcanic planet, and two gas giants; it has three of the best airless rocks in the game for setting up Refining and Fuel Production, especially if you don't want to settle in a system already colonized by a major faction; it pretty much always has at least one decent or better site for any colony item other than Soil Nanites; and a number of the potential colonies will always be close to one another due to being planet/moon groups and thus are relatively convenient to visit or defend. About the only real downsides I can think of for Penelope's Star are that it doesn't usually have arable land or organics, is rarely within range of a hypershunt, and doesn't have a gate, and those aren't very significant downsides.

Also, with nine guaranteed planets and moons, including one Very Hot and three Hot, it's one of the best places to set up if you want to make extensive use of AI cores on your colonies and don't want to be constantly running back to deal with AI inspections - very few systems have greater, or even equivalent, potential for military infrastructure.

Proximity to the core worlds, meaning expeditions arrive very fast, and the lack of food and organics is a dealbreaker.
If Ithaca has food and or organics, and there is nothing else that is better within the entire sector, I will colonize it.

The only resource I don't consider to be a dealbreaker if a system doesn't have it is either of the ores. Refining is cheap and profitable meaning it can be spammed, so even if one planet gets hit with a substantial ore trade disruption, the rest will be fine, and so metal demand will always be met for heavy industry worlds.

Also, it is incredibly rare that I find more than two cryoarithmetic engines per run.

[Megas]

Penelope's Star is good in that the planets are decent and next to a gate system (Magec) without patrols.  It is useful as a default or fallback if nothing better is found.  It is not great or optimal, but it usually has something acceptable that will satisfy demand (like volatiles).  If Penelope's Star had a gate, I would probably colonize it for a lot of games just for convenience.

As for dealbreaker, for me, it is if the system does not have a gate, or next to a system with one.

[Aeson]

the lack of food and organics is a dealbreaker.

How is the lack of food and organics a dealbreaker? There's little real benefit to having in-faction Food and Organics - even without using AI cores, you can import enough of either from the other factions to do anything except run a Cryorevival Facility at full capacity, so all you're really getting for having them in-faction is a small upkeep reduction - and Farming's usually the lowest-grossing industry, especially since it often cannot be boosted by Soil Nanites, so if you're optimizing a colony for income generation it's one of the least valuable things you can have on the planet once you start stacking multipliers.

Proximity to the core worlds, meaning expeditions arrive very fast

So? Expeditions are not that problematic in the current version of the game, the Core's possibly the least inconvenient place to need to go in response to an expedition, and even if you can't intercept or receive the expedition despite the rather generous amounts of warning you get for them it's no great loss to have a small colony disrupted for a time.

Also, once you're a bit more established, expeditions targeting colonies in Penelope's Star have to face down the collected military might of up to nine colonies worth of Patrol HQs, Military Bases, and High Commands. It is very, very possible that you won't need to do anything at all in response to an expedition targeting a colony in a developed Penelope's Star system - they're just going to run into your patrol fleets and die without you needing to so much as lift a finger.

[eert5rty7u8i9i7u6yrewqdef]

the lack of food and organics is a dealbreaker.

How is the lack of food and organics a dealbreaker? There's little real benefit to having in-faction Food and Organics - even without using AI cores, you can import enough of either from the other factions to do anything except run a Cryorevival Facility at full capacity, so all you're really getting for having them in-faction is a small upkeep reduction - and Farming's usually the lowest-grossing industry, especially since it often cannot be boosted by Soil Nanites, so if you're optimizing a colony for income generation it's one of the least valuable things you can have on the planet once you start stacking multipliers.

Proximity to the core worlds, meaning expeditions arrive very fast

So? Expeditions are not that problematic in the current version of the game, the Core's possibly the least inconvenient place to need to go in response to an expedition, and even if you can't intercept or receive the expedition despite the rather generous amounts of warning you get for them it's no great loss to have a small colony disrupted for a time.

Also, once you're a bit more established, expeditions targeting colonies in Penelope's Star have to face down the collected military might of up to nine colonies worth of Patrol HQs, Military Bases, and High Commands. It is very, very possible that you won't need to do anything at all in response to an expedition targeting a colony in a developed Penelope's Star system - they're just going to run into your patrol fleets and die without you needing to so much as lift a finger.

Lack of food and organics is a dealbreaker as it is tied to a colonies stability. Cross faction imports increase the risk of trade disruptions. A bad trade disruption on a low stability world, such as a commerce and or free port world, can significantly reduce the effectiveness of that colony. It also makes the player dependent on the core worlds, which is gross.

Multiple high commands can beat strong expeditions, until you get unlucky and get smacked by a very strong PL expedition in conjunction with a strong SD expedition.
I prefer to play safe rather than sorry, so I prefer to be as far away from the neighbors as possible. I will also admit I baby my colonies.