Things that don't make sense (v2)

Conjecture.  Maybe that was an aspect of the Crucible?  I don't have any better thoughts on the subject.  Of course, if it's part of the Crucible, which was allegedly the creation of countless alien races over many cycles, why was the Catalyst there?  To me, this never added up.  I honestly assume the Crucible was a creation of the Catalyst all along to trick some race that managed to survive into choosing Synthesis.  Or, possibly, it's a creation of the Leviathan to wipe out synthetics and leave the galaxy in a weakened state for them to take over.  The Catalyst then subverted it for its own purposes in order to survive.

Imo everything related to ME3 ending makes sense, at least on a general level.

THE CATALYST
The catalyst is an advanced AI, and it was created in order to solve the “chaos problem” (synthetcs-organics conflict, technological singularity maybe? etc).
The reapers are its current solution.

The catalyst controls the reapers (probably it's not the same "direct" control of Harb vs Collector's leader: the catalyst embodies the collective intelligence of the reapers, so even if the Catalyst can of course influence the reapers, every reaper mantains, within certain limits, a specific individuality, as Sovereing said).

The catalyst doens't direclty and fully control the Citadel. Not the arms and the mass-relay (the relevant parts) at least. Maybe it used to control it/them through the keepers (we know there is a strong connection between the keepers and the citadel/reapers), but we know that the prothean scientist from Ilos somehow broke this connction.
We never see the catalyst directly controlling anything, even when it would have been useful for its purposes.
The catalyst need Saren, the Sovereign, Cerberus, Tim and finally Shepard to perform “material” operations.
The catalyst is very likely unable to control the Crucible, too. Referring to the possibile choices that the Crucible provides, it says "I can't make it happen". So we can be almost certain that it needs Shepard to use the crucible.
So we can summarize the previous point in one general statement: the Catalyst is incapable of direct, relevant material actions, it can only influence/control the reapers.

THE CRUCIBLE
The crucible is, according to the catalyst, little more than a rude power source (from the catalyst point of view, at least), but in combination with the citadel it is capable of realising a huge amount of energy. So, it's not an hacking device or something similar, just a powerful weapon of mass destruction.
We don't know who designed it (very likely not the Leviathans, because the catalyst says, reffering to the crucible designers, "you wouldn't know them" -> and Shepard knows the Leviathans).
We only know that its design evolved many times.

THE CRUCIBLE DOCKING
This is the crucial moment. Once the crucible docked, Shepard is brought by the platform (which is probably part of the crucible) in front of the catalyst. The crucible is not working, it needs to be activated
The 1 million dollars question is: why the catalyst doesn't shut of the crucible or, if it can't “personally” do that (we have said that he is probably incapable of direct, material action), why doesn't it wait/order to the reapers to destroy it and to continue the cycle? Why does the catalyst seem to strongly desire that the crubile is preserved and activated?


The answer to this question is resumable in one sentece: the variables have been altered.

More specifically:

1. Its solution (the reapers) won't work anymore.
The Crucible has been proven possible and a real threat, that its mere existence as a tangible object - and not a dreamy idea - changes things completely because one day the Reapers will be defeated by it (and refusal ending proves it -> the stargazer says that "the reapers are no longer a threat"). Even if the crucible is not used, the reapers days are done, defeated by the next cycle or simply "fired" by the catalyst after completing the current harvest. They no longer have the strenght (they already had some relevant losses) to continue the cycle. The can complete this one, but not the next one.

2. The crucible changed the catalyst... created new possibilities.
The catalyst original solution won't work anymore, but new solutions are now available. All of them are better than the reapers.
- Synthesis: do I really need to explain why this is the perfect solution from the catalyst point of view? (N.B. for the catalyst this is the only true solution; the other options are both a makeshif at best, the lesser evil)
- Control: the reapers can be "upgraded" with a new catalyst 2.0 (the sheparlyst) and, thanks to Shepard's memories, consciousness, readiness etc, they can become somehow more effective, adapter to their new task of “peace-keeping”.
- Destroy: this cycle has proven itself worthy/ready, somehow special, and since crucible is a weapon that can destroy every single syntetic organism in the galaxy in few minutes, the organics of this “exceptional” cycle have proven that they can effectively deal with the synthetics threat (or, at least, better and/or longer than the reapers or other less special cycles). Another possibility is that if this cycle kills all the advanced synthetics, organics may gain the upperhand for a few decade, and be able ot explout this advantage.


This is why the catalyst helps shepard, gives him information, doesn't shut off the crucible and/or "stops" the reapers from immediately blasting the crucible.
The variables have been altered, and both shepard and the catalyst need the crucible to be activated, if they want to achive their goals.
The crucible docking, from the catalyst point of view, can be seen as the famous "last straw" (the catalyst finally acknowldge that the process, started with the prothean scientist of Ilos, is no longer reversible). Something very close to what legion say about the heretics ""An equation with a result of 1.33382 returns as 1.33381. This changes the result of all higher processes. We will reach different conclusions". A little difference with huge consequences.
So the catalyst want the crucible to be used before it is destroyed/becomes useless (there is no much time, and the game shows it: if Shepard doesn't act, the crucible will be destroyed), and he needs Shepard to do so.

In conclusion,
a ) IF the catalyst is incapable of direct, material actions
and
b ) IF the docking of the crucible has
- demonstrated that the Reaper-cycle solution won't work anymore
- provided better options

THAN the catalyst actions (and me3 ending) make some sort of sense.

Things that don't make sense:

Mass Effect 2 & 3's logos... who tf designed those things? They're god awful! Imo they clash pretty hardcore with the Sci-Fi style of the words Mass Effect.

Wait, really? That's hilarious when you consider how little Shepard cared about their own death and the two years they lost.

Okay, I would have loved to see how that draft turned out because that sounds gloriously silly and wonderful all at once.  

Because it had a hole?  It seemed like there was more to it and we were not getting an answer.  Legion had to have been on Alchera, meaning it followed Shepard there.

"She's a stalker" is the obvious answer.

Probably.  I don't hate her I just don't think she makes sense as a single character.  She doesn't have the relative age or experience to fulfill any of her roles - as a "super" archaeologist, as a top notch information broker, and certainly not as a squadmate on par with people who had trained as fighters.  As I said elsewhere, she could have worked in an Ann Bryson role or as a much older, commando-turned-archaeologist, but she failed to be realistic, even given that it's a science fiction game.

Yeah, her being "special" was part of the problem.  She was a little too special for my tastes.  If you're going to go with cute and sweet she shouldn't also be super awesome in every thing she tries.  Just my take.  And I wasn't asking her to be a stripper but the strippers don't start with asari commando skills.  Liara seems to have done so.

As for the geth thing, I thought I remembered hearing something about it some time ago.  Don't know the origin of the idea but it wasn't with me.

The only thing her background supports is her studying protheans. She has no training or experience in combat as the trilogy shows. There is no reason why she is the one helping recover Shepard's body. If it wasn't for Cerberus, she would never had made any attempt to go after Shepard's cbody. I would have let Cerberus be the only ones involved in recovering Shepard's body.

I do like the idea of Bryson angle. In ME1, Liara's job is to say Ilos. In ME2, she never shows up. In ME3, she's on Mars after learning the protheans  may have something that can be used to stop the reapers. After Mars, she is sent to Hackett. 

I've also mostly come to terms with accepting what actually physically happens in 3 on face value making sense... but it just doesn't make sense on other levels and some stuff like the Asari superiority, The Beautiful Tuchanka, Geth Pinnochios, "Mass Effect is totally about the fatalism of war", The Kid etc. etc. either feel tonally or thematically inconsistent with the previous games just in the way it's pulled off. I believe any story can eventually be anything it wants to, even Mass Effect, even Time Travel if need be... but everything, and especially the larger we go in ambition of idea, it has to be set up and executed upon properly. That's where ME3 fails and in a few key scenes woefully botches the storytelling entirely.

She is young by Asari standards but ancient by every other race's standards. That said it is clear that she is the squad version of an Adept. Someone who relies on biotics more then fire arms.  In that case she isn't a mary sue because she is an Asari and they all are trained to use biotics from an early age.  And it is clear she recived weapons training from Shepard and the rest of the crew. If during the retake the Normandy mission of the Citadel DLC you select Liara and Wrex he will mention if Liara still remembers that quick reload trick he taught her.

As well as the transition from archeologist to information broker isn't a sudden change. From the time Shepard picks her up in ME 1 and she realizes the significance of the Reapers she shifts gears into trying to gather information about them to help stop them. Given the 2 year gap between ME 1 and ME 2 that is more then enough time to learn a new skill. Given that spying and archeology do have some common ground. Like the fact that not all information is valid or relevant and learning what is true and what isn't is an important detail of both.  She only becomes the Shadow Broker as an impulse decision. And already has the well developed system in place to step into.

She didn't just go right from being picked up off a planet into the Shadow Broker.  There are reasonable transition from one state to the next and while they might be a bit accelerated she is no different in that aspect then just about any other squad member including Shepard. I don't see people complaining about Garrus's going from a standard cop to leading a small para-military unit that engages in covert lethal attacks on well established gangs with 100 times the resources as them in the very heart of their territories while only being taken down when one of their own betrays the rest of the group.