The incompetence of the Alliance and Council.

To be fair, they were dead regardless of Shepard's involvement. If you didn't own/play the DLC, Shepard still ends up in jail for working with Cerberus. Warning the batarians doesn't make any difference with the outcome, just with Shepard's moral compass. That said, Shepard shouldn't have been jailed for working with Cerberus. The Council gave him the okay, at least if you played Paragon or Paragade. While they don't have any jurisdiction over the Systems Alliance I would think that would at least give some leeway.

Despite everything I just wrote, I thought there was an implication that he was being held as a form of protection from the batarians and/or Cerberus.

A Shepard who has completed Arrival tells Grunt explicitly, "They locked me up to keep the Batarians off me." It makes sense, to avoid war, as everyone seems to agree in the posts I've read.

I just wouldn't have decided on Arrival as the transitional DLC. I didn't mind the destruction of Aratoht, since it was the right choice under those circumstances. I just don't think it was a great story. It ended up being a harbinger (lowercase h) of the hamfisted writing in ME3.

I hated the unrealistic focus on Earth in ME3, but whatever. So you need Shepard to begin the game on Earth. Cool. Why can't he be in Vancouver to meet with Alliance leadership? Maybe he's just now reporting on his activities with Cerberus? Maybe, if he doesn't blow up a solar system, he's been pursuing options in the intervening 6 months; and now he's debriefing after his latest outing?

I can think of all sorts of reasons for Shepard to be on Earth that don't require incarceration. It was a weird choice, but plenty of things got really weird or forced by the time we got to ME3. The writing went from attempting to be fairly sci-fi in ME1 to Hollywood rule of cool in ME3.

I don't mind the fixation on humanity. I dislike the fixation on Earth.

Way before the Reapers moved the Citadel, and before that possibility was even an idea in anyone's mind, Shepard was rallying forces to fight the Reapers save Earth.

Shepard's goal was rarely ever expressed as, "I need your help to build and deploy the Crucible." It was always, "Primarch, Earth needs the Turian fleets."

Major Kirrahe doesn't say, "You'll have my help defeating the Reapers." Rather it was, "You'll have my help retaking Earth."

It was ridiculous. Earth was not unique or special as far as anyone could tell before Priority Earth. It was just another homeworld under attack.

I recall thinking the "Take Back Earth" marketing was absurd for anyone who had actually played the first two games and understood the setting and enemy. I figured it was just marketing to bring in the Halo crowd; that is gamers who might like the series but hadn't yet played. Then, the ME3 story revolved around the same weird mantra.

I have no issue with the Reapers focusing on humanity. That was telegraphed in ME2. I took exception to the strange obsession that Shepard had with Earth, long before it made sense, when the focus should've been on stopping the Reapers.

It's because of Anderson. Shepard had to go back to earth to have that touchy-feely scene with Anderson. Look how stupid the beam run was. It was done like that so only Anderson and Shepard can be on the Citadel for the scene. Had the reapers left the Citadel where it was, that touchy-feely scene couldn't happen. It was all done for the feels.

I don't have a problem with Shepard saying this, that, and the other thing about earth, but it didn't make sense for the other species to say the same.

I've heard it said before that we wouldn't have been prepared no matter what. Vega said the same. Kind of irrelevant because trying was better than nothing. Even preparing for some level of survival is better than nothing. The Protheans managed, if badly, and we could easily have learned from their example. We even knew mini-relays could be built that were outside of Reaper control! So, yeah, they screwed up but there was no realistic way to stop them besides deus ex machina.
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Nah, it's better for the Shadow Broker to step away from her life of leisure to investigate artifacts on Mars. And only begin to figure things out in the nick of time! 

Finding out about the  Prothean weapon should've been the plot of ME2.

The entire purpose of the Council seems to be to act as a foil for Shepard. They're the comic relief. This especially applies to Udina until ME3. You're the cop in an action movie that goes around blowing up everything but always gets the bad guy, and they're the angry captain who does nothing but yell at you.

God, some little kid in the neighborhood let out a scream or rather a screech that sounded like a banshee. I looked out the window and they were just playing like normal. Kids today.

Of course he's like that. He realized what a colossal idiot he was in discounting everything Shepard had ever said about the Reapers.

Except Anderson. They ignored him.