Well, except for the batarians who, you know enslave the humans they don't outright kill, while the Council goes "Tut-tut, you really should have defended your colonies better" 
Actually, the Hegemony doesn't do that, per se. Rather, they secretly sponsor various pirate groups to do the job; those were the enemies at Elysium and Torfan. Bring Down the Sky becomes a bit confusing, admittedly, because one would think it'd count as a bona fide act of war against the Alliance... which makes me suspect that Balak was the only one there with an official connection to the Hegemony's government, which would explain why he wasn't part of the original raid and more or less hijacked it.
Mr. Cyborg Saren.
And very little of it able to be colonized. Anything else would get into what the Council claimed, the Batarians legitimately or illegitimately claimed, or beyond relays that again, they're not allowed to open and use without the Council getting into it.
That's why the Collectors attacking was so bad. Humanity was forced to expand into the most dangerous parts of the galaxy in order to have any sort of significant colonization effort (beyond like Terra Nova and Eden Prime and such). Resources are plentiful, yes, but not places to live and expand presence and influence as human organizations and populations wanted to.
In this sense though, they were a Krogan-lite situation. This is why the Council was so... iffy about humanity. Are they another Krogan? Or on the other hand, maybe they're another Asari? Or maybe Quarians? Or maybe Batarians? Or Turians? They just can't pin humanity down, so they both welcomed them but treated them with kid gloves. Thus the frustration on the part of some Alliance/Human leaders - "Do they want us all-in? Or will they leave us alone?", sick of the wishy washy.
IIRC, Saren's implants were supposed to only be there in the final battle, but they dropped the non-implanted version of his model without changing any of the dialogue. The result is rather wonky, especially when Saren is bragging about his implants during the final battle while having not changed physically at all.
Also, the human colonies being attacked in ME2 are, by and large, not part of the Alliance; they went into the Terminus Systems, not to help humanity expand, but to get away from the human governments.
::shrug:: In a liberal 21st century audience, probably wouldn't go over very well. People get crucified over tactless or poorly thought out statements all the time.
But what keeps getting forgotten is the second half of her statement "...but Cerberus has a record of being extremist"
Ash is "not a fan of" aliens. But she's nothing like the real fringe lunatics that are out there.
I don't know where you get the impression that I think she's a fringe lunatic. I don't think her speciesism is terribly uncommon; that does not mean that it doesn't exist, it just means that many humans are speciesist.
Xil, do you just want the Alliance and Human governments to merge with the Asari and get it over with?
EDIT: And I say this as someone who has the ultimate view that the whole galaxy should unite into one, mind you. I also am not as scared of an IRL world government as many others are.
Right now, no; far too soon.