Things that are annoying

I never saw any kind of monetary system within quarian society. No saying it isn't there but I never saw it. Could be the quarians are primarily concerned with the survival of their species and A/C for a suit would be considered a basic quarian right. Fact is, they can't afford to be reckless with their own people. Remember, they won't even imprison or execute other quarians. The worst is exile so any children they have can one day join the Migrant Fleet.

Not sure. All I know is that if peace is achieved between the quarians and geth that the geth will begin the process of repairing the immune systems of the quarians. That means it's a problem that can be fixed. (Sadly, I always pick Destroy and that puts an end to the geth, even though I generally make peace.)

However they felt about the quarians, they still knew that their creators wanted them destroyed. There's no incentive to welcome them back. They would have to assume that if the quarians were given a home and were able to build a population and colonize that they'd eventually come after them again.

Do we know that they don't have an attachment to the place? You could say the same things about any race where its people choose to colonize other worlds.

Not with a synthetic race like the Geth. We know their needs are different from that of an organic's. We know Legion himself tells Shepard that to treat the Geth like an organic race is benign racism and goes further to explain how organic offspring takes time to develop whereas geth require far less. Their pragmatism is the most notable, with the explanation of lack of windows. So an attachment to the home world is not confirmed nor is it logical as it places them at a target area of the creators. Had they built their dyson sphere elsewhere, they wouldn't have lost so many programs.

masseffect.wikia.com/wiki/Geth

"The geth are reclusive and secretive. This is partly due to their synthetic nature: They have no need to interact with other races because they do not share the same goals, needs or instincts as organic species. As machines, comfort is also not a concern for them, something that is reflected in elements of geth ship and station design (e.g., minimal gravity, lack of windows, efficient use of space, function over form, lack of atmosphere, and absence of climate control).

According to Legion, geth do not actually live on any of the quarian planets they conquered, serving merely as caretakers for them instead. They find it more efficient to live on space stations and draw resources from asteroids, though they maintain mobile platforms on the worlds to clear rubble and toxins left by the Morning War."

- Having to listen silently without contradicting when
1. Eve spouts her BS on how the genophage is responsible for all the krogan's problems and how curing it will fix everything.
2. Mordin considers sympathy for Eve to be "new data" that invalidates his genophage work.
3. the krogan whine about how the genophage was wrong when the alternative for every other species was to just let the krogan dominate them.
4. Chakwas brushes off Adams not joining the crew in ME2.
5. the new council in ME3 says Shepard sacrificed the old one "to protect human interests" when it was because a reaper was glued to the damn Citadel.
6. every short-sighted crew member scolds you for keeping the collector base in ME2.
7. Jacob brushes off cheating on you in the Citadel DLC by saying you were with Kaidan/Liara when they met.

- Having to keep saluting Hackett all the damn time and appearing to like him even though he:
1. spoke against you becoming a spectre unless you're a war hero.
2. makes sure no arrests are made for people defiling the Torfan torch (ruthless background).
3. sells you out to the batarians after Arrival to keep his hands clean.
4. steals your spotlight by boarding your ship with weapons-drawn soldiers and makes the final speech when you united the galaxy while he presided over the most devastating defeat in human history.

- Being forced to
1. let Ranos Thanoptis go a second time.
2. let characters like Shiala, Ranos, Suresh, and the rachni queen go scot-free, or execute them.
3. be fine with an AI controlling the Alliance's most advanced warship.
4. be fine with Liara blatantly spying on you.
5. turn yourself in to the Alliance before ME3; even for something as bogus as "working for Cerberus."
6. be absolutely convinced of Saren's guilt and the reapers' existence with almost no evidence in early ME1.
7. be relatively ok with Jacob cheating on you and getting someone else pregnant until the Citadel DLC slap scene.
8. be a spectator to the Kai-Lang/Thane duel.
9. stupidly put down your weapon in the Citadel DLC because cloneShep took Brooks hostage.

- Not being able to
1. point out to Samara threatening renegade Shepard that she's quite renegade herself.
2. beat down the greedy black market weapons dealer salarian in ME3.
3. suspect EDI intentionally let the Collectors locate and board the Normandy so she could be unshackled.
4. criticize Liara for not joining the crew in ME2 so she can sit at her desk on Illium plotting revenge.
5. call Jacob a moron for honestly suggesting to space Legion. After that, he shouldn't even be allowed at the meetings.
6. punch Jacob when he selfishly wants "a life" and "a family" in the middle of a reaper war, refuses to rejoin the crew so he can be a glorified bodyguard, and having the nerve to say "the Normandy is your real love."
7. tell Miranda that stopping the reapers from killing everyone is far more important than finding her sister.

- Obvious one: The Horizon survivor bitches about you being with Cerberus after you just saved their life and the colony's.
- ME3 Mordin has a crisis of conscience at the worst possible time; effectively standing between you and salarian aid, and even tipping off the krogan in the first place about the fertile females without being able to ask why he'd do that.
- Liara stupidly asks what's bothering you shortly after the reapers invade earth. How would she feel if you asked her that when she was crying on her bed after the reapers hit Thessia?
- Kasumi complains about Shepard wanting her to actually fight to save herself and the galaxy.

Why would he join Cerberus? Honestly, Chakwas doing so is outright baffling. Joker makes sense since he was grounded by the Alliance.

I never had this happen. Shepard certainly wasn't in batarian hands by the beginning of ME3. He was supposedly confined specifically so the batarians didn't kill him.

I think it makes sense in the context of being an LI. If that person is simply a squadmate there shouldn't be nearly as much hard feeling.

More along these lines, he was a total dick when he told Tali not to forget to introduce herself to the ship's AI.

--some observance while on some groups...

I'm not sure why people who gleefully repeats "you big stupid jellyfish" and then at the same time getting really mad at Ashley for being racist for having trouble differentiating aliens and animals.

Garrus and Tali being on the roster in ME3, even though both can be dead, and not any of the ME2 squdmates that aren't ME1 characters

I would have Garrus and Tali not on the roster in ME3. He would be Victus' secretary until the genephage is dealt with and Tali plays the same role as Xen and Raan.

I believe its been mentioned in the things that don't make sense thread. I know it was mentioned on the old forum

Sure, it was a  mistake on Bioware's part (an undeniable plot hole, iMO). 

Still, why make out like it's some sort of personal insult and allow it to annoy you for 10 years.  That "ship crashed 10 years ago." (joking - just couldn't resist).