Things that don't make sense (v2)

Well, I figured that was the implication from your sentence. Anyway, whether that particular word fits or not, I think you made it clear that you don't exactly see that action as an indication of competence on her part. I am just saying, one might as well interpret it as bad luck while she chose the most appropriate actions in a tough situation.

After all, if the bubble she didn't know about hadn't activated, she'd have been able to take the lift up, bypass most of the enemy force and almost would have gotten to the surface. whether that would have worked out or not, given the extent of troops that were on Therum is questionable but she couldn't know that yet. So as far as I can see, her actions were perfectly appropriate.

She may not have professional combat training but then, what's your point exactly? Are you saying that makes her unvaluable as a squad mate, despite the fact that she is clearly the most powerful biotic on board the Normandy? What then of other squad mates who didn't go through any form of official training like Kasumi, Jack or Tali?
As for her "slow reaction" in some scenes, throughout the trilogy (and depending on what squad mates you choose), pretty much every single character (including Shepard) can have a scene or two where they just look dumbfounded at a YMIR mech or a gunship before reacting for dramatic effect.

Besides, if you don't want to have her as a squad mate, don't use her. The only missions she absolutely needs to come along is Mars (because she knows the place and has the info about the archives, not because she's a great soldier), Thessia (here I would agree with the point that technically, Shep should have been able to say no to her request to come) and LotSB (where the entire quest is about her).
I really don't see the problem on a logical level here.

Right, so if the only problem is Thessia, then well, that I can sort of understand (though I really don't mind it as much and just go with the flow on that one). Otherwise, as I said, I don't see a problem, really. For me, it's fine to take a squad mate that doesn't have official training, as long as I think they can still handle themselves in a fight (which Liara absolutely can). The "blink of an eye" mistakes can also happen to trained soldiers after all and all the squad mates you dismissed there can bring other potentially useful qualities and expertise to the team (if not gameplay wise, at least lore wise).

Which is why, like suggested Mordin could have done, she'd be better as a go-to on Prothean topics while someone like Shiala head out into the field.  (Never mind that Liara didn't know the real truth about the Protheans; no one did.)

I guess it's because of Udina.
Can you imagine the Councilors' joy when they'd have to hear his outrage for an entire afternoon, just because they fired Shepard?

Instead they wait until Udina basically got most of what he wanted and he himself is petitioning for Shepards grounding.

Did Shepard let Saren get away? Even without Shepard, Kirrahe would have detonated that bomb. It was him and his team that came up with the idea. I agree with Udina not wanting Anderson to interfere in the case because of his past history with Saren. The only valid point the turian councilor makes is when Anderson brings up Shepard's visions. If the council fired Shepard, or used another spectre, it wouldn't stop him/her from going after Saren. He attacked a human colony.

Ok. So, did Shepard let Saren escape?

All assumption just as I what I said is assumption, but I doubt he would've waited forever. He also mentioned that it was unlikely that they would survive so having his ship to leave Virmire I would guess wasn't an option for him.

Anderson was fired for what happened at the facility? The only thing that happened is he was no longer considered to be a spectre. Hard to be fired from a position that Anderson never held.

If Shepard stayed on Virmire long enough to continue the fight with Saren, the bomb would not only kill him/her, but possibly destroy the SR1.

OK, I read your response earlier and see that I more perused your comment rather than read it closely (in regard to the above referencing ME1 alone).  But there are some other things.  When did Anderson get fired?  Do you mean as captain of the Normandy?  That wasn't even really anything to do with Anderson so much as Shepard becoming a Spectre.  If this is a reference to being on Earth in ME3, I always figured Anderson resigned because he did believe in the Reaper threat and wanted to humanity to be as prepared as possible.

I do agree that there should have been repercussions for hanging up on the Council but, honestly, Sparatus needed to someone to ignore his rants.  Sparatus is probably the most anti-human in the entire series, though I think he's a relic from the First Contact War.  (Funny how, if he survives, he's the one most willing to direct Shepard to get help from the turians.)

I can hazard a guess here, but it's only a guess. By the time Shepard became a Spectre, the Alliance had been part of galactic society for, what, 26 years? Now dial that back to when Anderson was much younger and we're really only 5-15 years in. The Council might have looked at what happened and saw this as a general weakness in humanity, like we weren't ready to do whatever it took to succeed. In contrast, Shepard wasn't afraid to tell the Council they were wrong to disagree until Tali came up with the evidence. To top that off, because they knew they'd screwed up, and that Saren was proven to have gone rogue, they figured Shepard was the one to chase after him. (Plus, we know Shepard was a Spectre candidate before any of this happened.)

You're right that Shepard didn't do things the way the Council would have liked, but that's not really the business of the Council. A Spectre has a LOT of autonomy to do the job. Also, Shepard went exactly where the Council suggested: Noveria, Therum, Feros, Virmire. I do agree that the option to hang up on the Council was stupid but there it is. They did finally temper Shepard's actions not because he wasn't chasing Saren anymore - he was - but because they thought Shepard was in the wrong about the true objective. Also, even with autonomy in place, the Council can call an end to an operation. If Shepard had said nothing about the Reapers and Ilos, he could easily have gone there. They just felt he was on a "wild goose chase" and that there might be better things for him to focus on - like Saren and the geth arriving with a fleet.

Anderson never made it past being a candidate and I have to imagine that most people don't make the cut (in their eyes) to become a full on Spectre. Anderson wasn't so much fired as he didn't perform as expected. This was colored by the evaluation but Saren who made it seem like Anderson was incapable. He wasn't fired; he never had the job. It was fitting that Shepard got the job for pointing out that Saren was a traitor. Maybe this was even sort of a way of expressing their past mistake (though it might not have been the same councilors) and showing that humanity was actually ready to do their duty.