You are forgetting Shepards death and the Lazarus project.
Or the Collector ship (idiot balls galore)
Or a whole slew of toher unanswered questions (where did Morodin get the bug? Why are guardian lasers not lasers? Why aren't they used agaisnt he occulus? Why do they go trough Omega 4 blind?)
1) sounds like personal preference. Would you have preferred Shepherd be all of a sudden "hurr durr I'mma work with Cerberus now" out of the blue? Didn't think so.
Nah, it's simply horribly done. Sheps death as a plot device is compeltely under-used. It has NO impact on the story. Shep's like "I was dead. No I'm alive? Cool." and forgets about it. It goes nowhere.
Frankly I tihnk it's nothing mroe than a cheap marketing stunt (the KIA trailer).
Either way, if they wanted to keep Shep out of action for a while and explain why he works for TIM, they cfould have done it in a bajjilion better ways.
Have Shep in a coma (and not broken, dead and rotting on a planet for a month
before being MAGICLY revived). OR have Cerberus retrive Sheps body and put it in stasis minutes after the fall.
Or friggin use Sheps death in the story. It make more sense for your former allies to not believe you are still alive (thinking you an impostor), so you don't get support from the council and that's why you go to Cerberus. Not this "Yo Shep. I heard yo was wroking for Cerbereus, so we all hates you now!"
2) explain please.
Worst trap and worst data retrieval in history.
The collectors decide to let Shep go that deep into the ship - in a room with plenty of cover. They let him reach one of the main terminals. They didn't block his path back or destroy his shuttle. And the best thing they can think of to spring a trap is to send a bunch of guys with guns. They didn't evne bring enough guys (tehy should have a massive numerical advantage)
Shep, the idiot that he is, takes no precautions. The Collector ship is powered down? How about making sure it STAYS down before you board it. Cripple it's engine and main gun while it's helpless.
Do I really need to go on?
3) You get him one on the planet you meet your former squadmate on. I thought that was pretty bleeding obvious. Guardian lasers aren't lasers for the same reason ML-16 lasers aren't lasers; because the word laser sounds cool. Do you think you could hit a target that small that is maneuvering that wildly while you're moving that fast through debris field as tightly clumped as that? If yes, you left reality a few parsecs back.
No. You get to the colony AFTER Morodin creates a couintermeasure (from a captured bug).
Aparently, Collectors left no traces of their presence before. So where does the bug come from?