How do we know that the NCR are really good guys?
I don't think there really is any 'good guys' in the world of Fallout. Even the Followers of the Apocalypse have done bad things in the past to get what they want. The New California Republic is just like any democratic republics in real life, they offer relative stability and political freedom in exchange for corruption and imperialist tendencies. They are just another shade of grey like everyone else. But they are the lighter shade.
They insist on wiping out the BOS unless you are very diplomatic,
The NCR's hatred towards the BOS is totally justified. The Brotherhood of Steel started the war in the first place since they think that anyone that is not part of them are 'unworthy' of technology. The NCR has tried to be diplomatic with them but things didn't work out. Plus if it wasn't for you, the BOS have no intention of negotiating peace either.
they want to turn New Vegas into a police state,
Not anymore then Mr. House or the Legion is going to do. Plus the NCR is actually a democracy, after the region is safe, they will likely allow the people of New Vegas to select elected representatives to join the NCR Congress. Plus in world full of raiders, mutant monsters, and that everyone can own laser weapons, is there anyway to have a functional government that isn't a semi police state?
they enslaved 'criminals' by the scores to work on their railroads,
The members of the Powder Gang are actually dangerous criminals that deserve their sentence. They are not political prisoners like the ones in the Gulag. Plus the just of convict labour is legal even under real life international law.
they have wiped out at least two towns (The Squat and Bittersprings) and have no inhibitions about further destruction all in the name of progress.
No they did not. The cannon ending for the Squat at Vault 15 is that they peacefully joined the republic. Even in the worst ending for the Squat, the NCR still didn't invade then. If the NCR wanted to, they can easily overwhelm the Vault and take it by force. But they actually preferred to do it the peaceful and dipomatic way.
As For Bittersprings, the situation is just like the war with the BOS. The Khans are by no means an innocent group. They have been enemies of NCR before the republic was even founded. If it wasn't for the Vault Dweller's intervention in the first game, they would have wiped out the NCR in it's early years. Even after the republic was founded, the Khan have spent years trying to overthrow their government and sabotage them from within (using the Vault 15 Squat as a front to attack NCR's supply lines). After the NCR expansion reached Nevada, what was the Khan's first reaction? "So, the NCR is moving into the area, this is awesome! Lets rob, murder, pillage and [censored] their civilian settlers as they struggle to get a foothold. Just like we did in the good old days! On top of that, lets sell highly addictive drugs and make the wastelands an even worse place to live!" But to the Khans surprise, the NCR refused to just sit there and take it like they did back when they were still Shady Sands. They fought back and attack their main settlement. The NCR's actions were regrettable, but a society that lives by the sword, dies by the sword. You can't make a decision to be raiders and thugs and cry foul over the consequences when your innocents get caught in the cross-fire.
Has anyone actually talked to Aaron Kimball? The guy has 'Enclave Lackey' written all over him.
Which dialogue are you talking about? Will you mind clarifying?
Before the war the Enclave were proficient as a shadow government and just because they were defeated in FO2 doesn't mean that they are all gone. How do we know that they didn't secretly take over the NCR and are furthering their goals under the flag of the two headed bear? In the original FO3 (Van Buren) FOVB the main badguy was a rogue NCR scientist who wanted to continue his pet project which sounds suspiciously a lot like the unrealised goals of the Enclave. It would not suprise me if the "Broken Steel" of FONV features this maniac as the face of a sect of Enclave secretly running the NCR. There is more evidence to be uncovered in this time-honored tradition of deceit and intrigue of the diabolical Enclave.
It is possible that the Enclave still exist within the NCR government. But there is not evidence to support that. Under the Burden of Proof, we are not called upon to prove a negative. Therefore until you can show evidence that the Encalve are in control of the NCR, the default position is that it isn't the case.
It is really sad for me to see that people who consider the Yes Man/Independent path to be the ‘best’ ending for New Vegas so desperate to find reasons to hate the NCR. So far on this site and the NMA forum I have seen people making claims about how the NCR is communist, or that they are secretly using slavery, or how they are worst then the Legion, and my personal favorite, about how the NCR is bad because everyone should become tribal… etc. Anything that ranges from examples of ‘Did not do research’ to ‘Blatant lies’. Can’t the NCR haters find any legitimate points to support their debates?