... Where to begin with this....
*****Holy Hell Wall Of Words Alert******
"If you do kill a character in the opening scene, then you'd expect the game to be that character working through the experience and growing as a human being. But Shepard is up and capping robots in seconds, and the whole "I was dead" thing has no impact on him as a character."
Last I checked they knock your previous Lvl 50 super shepard back down to lvl 1, for the chuck noris of mass effect, id say thats relearning everything you became. And capping a couple of weak androids as appose to Swarms of Geth Primes sounds fair enough of a "death hangover".
"They claim that all of the Cerberus agents you encountered in the previous game were "rogue elements," but that doesn't make any sense because this new Cerberus is both too competent and too focused to have countless rogue cells wasting resources and working counter to Cerberus goals."
I know you payed attention enough to the plot to see how many times Rouge cells would feed false reports to the Illusive Man, Hell Jacks Loyalty mission Case and Point. When your busy with world issues I think you want to leave the small stuff to your cell block commanders.
"Their trap depends on Shepard being an idiot and personally boarding their vessel, instead of blasting the ship at a distance or sending in a team of subordinates. "
Really? Ok I need to know how to get through the Omega 4 Relay, Let me just nuke the ship that can tell me how.. Great idea. Or better yet Let Chuck Norris Sit this one out while I send Tali and Mordin to go figure out how they do it on a supposedly inactive ship.
"They have the drop on him, the home field advantage, superior numbers, a more advanced ship, the guidance of a Reaper, and they still can't kill him, thus establishing themselves as bumbling fools. Worse, they didn't even need to beat him in a gunfight. They could just have flown off with him and left the Normandy behind."
If you listen to 1 of the 100 Times Harbinger talks he keeps saying "Preserve Shepards body, Preserve Shepard if you can", They wanted him for their human reaper, not dead. As for flying off if you payed attention they waited till they (tried) to Fry the Normandy so he couldnt not escape while they powered up the engines. But Edi Saved the Normandy from the surge and shepard escaped just before their engines came online. It takes a while to Power on and Heat up Colossal Space Ship engines, Its not like turning on your ceiling fan.
". His plan requires that Shepard blindly walk into a trap and escape anyway, which means his plan hinges on the gross incompetence of the enemy."
His plan relied on EDI to be Fast and Shepard to be Strong, Both of which are WELL known for those skills. Not only that it was the ONLY way to gain the info about the Mass Relay. If they had just went to the Reaper they wouldnt know what they were looking for or why. It was a necessary risk or the plot could not have advanced.
"Why didn't he blow up the supposedly helpless ship? Why didn't he look for the bridge / engineering and try to take control of it? Why didn't he have explosives for wrecking the ship once he was inside? What was his goal? What was he planning on doing if there hadn't been a trap?"
His Goal was a hell of a lot safer than your idea. "Get in, get the necessary data, GTFO". Seriously "Lets just bring 100 pounds worth of explosives on our back in a ship that could come online at any minute and fly away with us onboard". Even with that much a platoon worth of explosives would not be enough to take that thing down unless you fight your way to the correct spot (which btw they only learned BECAUSE they data mined the trap). Quite frankly when the ship that ripped my old Ship to shreds in seconds is powering up I wouldnt want to just chill and see if I can take it over somehow (I mean, let the 3 man team just fight their way to an unknown command point and fight off the entire collector fleet while the Normandy gets ripped to shreads, excellent idea.)
"Later, The Illusive Man finds a derelict Reaper. (And in classic Cerberus style, he sent a bunch of scientists on board without ever checking up on them, leaving them to die hilariously in the name of Idiot Science.) "
He said he lost contact with the crew that was working there, I think that means he was talking to them, Unless you think it went something like "Hey, Miranda, remember that crew i sent to the reaper a month ago, yea that one, you mind checking up on them? I kinda forgot about them. What no contact? O well, back to banging super-models"
"Remember that one of the great challenges that Shepard is facing is that nobody believes in the Reapers. So here we have one, all of a sudden. Then Shepard boards it and ... blows it up? How about taking a video and putting it up on YouTube, Shepard? How about offering tours?"
Great idea, IF he wasent TRAPPED by the reapers internal barriers. Or did you forget that the reaper locked him in there and the ONLY way out was to disable the reaper. As for video, i do agree with you on that one, would save him a hell of alot of headaches if he just got a helmet cam.
"But, if our only goal is to kill them, then why go to all this trouble to pass through the dangerous relay and fight them on their home turf? Why not just sit on this side of the relay and spawn-camp them? Maybe put down some mines for good measure.
In fact, why not just blow up the relay?"
Great idea, lets just pull up a lawn chair and crack open some beers while the reapers decide to show up, not like that base could help us or anything? Or you know, they might have more than 1 Relay, Hell they only damn well built the things, but who keeps spare relays or the ability to make them right? 2 Exits are for chumps. Real galactic super-beings only use 1 exit.
And BTW the goal wasent to kill them, (at least the Illusive mans wasent) The goal was to capture the base and see what they know. (Or be a idealist and blow it up because we do things our own way).
They are not plot holes in the least, Just because Cerberus dosent think like you dosent mean its a gaping plot hole. The game is actually very tight (at least ME2 is).