Things that don't make sense (v2)

It wouldn't be hard. Have the asari councilor mind-meld with her to see that she's not lying. If they can believe the audio file, I don't see why they wouldn't believe her or at least consider what she said. I could see them suggesting having her as squadmate to help Shepard stop Saren. She may have additional information that she didn't mention that could be helpful.

B G R

Everyone points fingers to this point while tapping their shoe with a grimacing face looking down at tiny BioWare and going "What is that >"

But I need to make my own incisions as to why this is less believable than offers to put games onto your account if you give someone your password...

This device we've spent so much time creating, was never designed to work unless a specific person of a specific genetic code would find out that the only way to make this huge machine work is to :
•Destroy part of it while it is active.
•Jump right into the middle of it.
•Hold onto your dear life to a big tazer.

While many others address the bigger issue of this ending, I am stumbled by the fact that this device, THIS HUGE MONOLITH, has to be severely damaged or abused in order to work properly.

Has nobody read the instruction manual ?
Did they skip past the 1067th page where it said "Upon activation please insert a genetically evolved organism straight into the focal aperture of the bridge, or blow the field resonator to hell with a weapon, or offer a sacrifice to the mighty electric company..."

Furthermore !
If there is some logic to a LevoDNA chain being inserted into the beam which somehow makes it work (I guess the Russians built it, russian products always require you to slam them with something before they work right) then what is the guarantee that DextroDNA organics won't suffer drastic consequences because their organic chain was not implemented completely into the protocol ?

TL;DR>
The final choice is always a problem, but the input design is even more senseless.

I think it can use the crucible as opposed to killing everyone again.

Maybe it's the Catalyst that's the problem. If the Catalyst doesn't think you're ready to Go Green then it won't offer you that option. We saw walls moving at the chasm. No reason to think that's not possible when it comes to the offered choices.

Then again, credit to those same engineers for building a beam of light that when a person jumps in, somehow manages to cause every organic being in the galaxy to suddenly sprout circuit boards.

Oh, hush, synthetic are superior to organics and you know it.  Otherwise why else would they inevitably turn on organics?  It's inevitable 

If Shepard does not complete the missions related to Zaeed, Kasumi, Grunt, Jacob and Samara, in ME3, their names will be seen on the memorial wall after Cronos is completed. For some reason, Zaeed's name never shows up even if he died in ME2. Anyways. How would they know they're dead to put up their nametag?

Who confirmed  their death to put on the list? 

How would Hackett know if Grunt is dead?  How about Samara? How about Jacob? Did the Alliance go to theses places? Those missions can be completed before Cronos, depending on the playthrough. So from the start of the attack until Shepard gets back from the mission, the Alliance was able to somehow confirm their deaths? I can see Kasumi and Zaeed since their death's are on the Citadel.

Who confirms it in any war?  It comes from various sources, still keeping track of the dead is just part of it all... an administrative task.  After all, each soldier has family, estates, a paycheck that needs to be stopped.  Often it's the medics who "clean up" a battlefield and collect the dog tags or other forms of ID.  Even though Grunt and Samara aren't Alliance, they belong to allied forces and there would likely be some sharing of lists among those organizations.  Admittedly, the game isn't great at giving the player a sense of a battle with numerous "other" people around - reporters and medics and such.  It even jokes about it... Shepard always feeling like he's "alone" in this war.  Jacob... well, if Shepard doesn't collect the scientists... what does the Codex say... do some of them survive and still defect to the Cruicble?  (IDK).

No one knew Jacob was with those scientists. The mission isn't completed. He dies. Did someone go that location afterwards? Look at Samara. Did anyone know she went to deal with her daughter? With Grunt, Wrex or Wreav knows he's dealing with the missing scouts. Since those missions can be completed right before Cronos, how would anyone know they're dead between the attack on Cronos and after the mission to see their names on the wall?

Someone knew - Samara belonged to the Justicars.  Someone would "clean up" those battlefields after the fact and report a list of ALL the dead they find that they can identify in some way.  In an AI riddled society, the communication of long lists of dead to all ships in the fleet probably doesn't take very long and would take EDI an instant to read and pluck any names she recognized from them and tell Shepard (or some other crew member in charge of the Memorial Wall) about it (and it's only after the very end that EDI  might be out of commission).