-The Rachni Wars were a legitimate thing. Read your Codex,sometime. The Rachni were under the influence of the Reapers. Due to their hive mind,only the Queens needed to be Indoctrinated in order to control the whole species. Noveria's experiment outright TELLS you this,and you see the proof in the pudding with the mad Rachni drones,who were separated from the Queen,and thus went insane. The Krogan were uplifted by the Salarians (a bad habit of theirs,actually.) to fight the war that they couldn't win (The Salarians made first contact with the Rachni,and so the Citadel saw it as THEIR problem to solve),so they were given nukes,rockets,FTL drives,and mass accelerator rifles. It worked. The Rachni were (believed to be) wiped out. Galaxy saved,and the Krogan were honored as heroes. The Rachni Wars was an Extinction War. Loss was total annihilation. The only way to win was to kill the Rachni to the last,lest they come back. This was the only view available to the Council. Hell,the Turian Councilor has some choice words with you,should you release the Queen. Something along the lines of "Are you crazy!? They nearly wiped out the galaxy!". Of course,he also chews you out for killing her,so... Schrodinger's Rant,I guess. W/E.
-The Krogan. Where to begin? Let's start with their evolution. On a DEATH WORLD. Before the invention of gunpowder,the most common cause of death was "Eaten by animal." Afterwards,it became "Death by gunshot." Their culture venerated great warriors and wise leaders. They became violent because they had no choice. Kill or be killed. Their culture was quite a thing,though,if the ruins you take a stroll through in ME3 are any indication. Mummies,man. They HONORED their dead. However,their evolution on a death world mandated something. Explosive fertility. When so many will die,the only way for Mother Nature to ensure their survival was to make them give birth in bulk,and gestate rapidly,on top of their famous redundant bodily systems. They evolved to survive Tuchanka,so,when they were given other planets to colonize,the Council very rapidly learned that the Krogan population threatened to overflow the galaxy,and with their warrior culture,they needed something to fight. So they turned to their neighbors for that fight,and took their land. The Salarians developed the Genophage,a bioweapon carefully crafted to limit Krogan growth. But,they lacked the balls to deploy it,so the Turians did it,instead. When the Krogan were fighting for control of Palaven's moon. Wanna know the significance of this? Palaven is the Turian homeworld. As in,the single most deeply entrenched position in Citadel Space. The Krogan needed space,and when they asked,they were denied. So,they took it. After the Genophage,the Krogan devolved culturally into what you see now,with very few sane ones,like Wrex. (Shepard.)
-Let me tell you a story. It's called the Morning War. The Quarians developed an advanced Virtual Intelligence to control a robotic labor force. This is common in the setting. However,what made the Quarian VI so impressive was the ability for every unit to simultaneously share and process information. One VI platform was near-worthless,and needed constant input. It was almost remote control. But,a dozen,or so? Autonomous. The Quarians continued to develop the VI so it could handle more complex tasks. As a result,the drones became more capable,and "intelligent." They eventually became capable of speech,though initially it was limited to the usual "How can we be of service" and "Acknowledged." By this point,the VI was dangerously close to becoming a full-blown AI. An AI in the Mass Effect universe is defined as a digital intelligence capable of true understanding,learning,comprehension,and growth. Or,in short,a digital mind that could operate like an organic one. Due to every culture ever having a culture (Wonder how that happened...) with their own entertainment sector,they all likely produced a large number of science fiction works revolving around rogue AI's,and so the Council put very heavy restrictions on AI development. The Quarians knew this. They also believed themselves to be on the verge of a breakthrough in the science,and believed that they would be hailed as the people who made fully controllable AI. Eventually,one of the VI platforms,without prompting,asked a question. "Does this unit have a soul?" What followed was a frenzied panic,on BOTH sides. The Quarians knew that such questions mean that the intelligence had free will,and could not be controlled. This meant that they were now in FULL violation of Citadel law,which would mean some serious punishment. In an attempt to get a lighter punishment when this all goes public,the Quarians started deactivating and destroying the AI and all mobile platforms. The newly-born Geth didn't understand why their creators,which they venerate,were attacking them,but wanted to live,so they fought back. The end result was the Quarians being pushed off their homeworld and colonies. As punishment for the Quarians playing God (or trying to),the Council declared them to be no longer part of the Citadel. Their embassy was removed. Furthermore,laws were put in place regarding the newly formed Migrant Fleet,the new home of the Quarians,effectively painting huge swathes of the galaxy as no fly zones for it. The Quarians,who already had weak immune systems,due to the lack of insects and other factors on Rannoch,were further crippled by their new existence aboard sterile ships. Meanwhile,the Geth didn't pursue,nor eradicate,the Quarians,because they feared what would happen if they did. When Mass Effect 1 rolls around,Saren and Sovereign use them as shock troopers,further souring what the galaxy thinks of the Quarians. Sure,the Quarians get SOME undeserved flak,but they earned a good majority of it by not watching and reading their versions of "I,Robot". Side note: My two most dear species in the Mass Effect universe are the Quarians and Geth.
-The First Contact War. This was a conflict of jumped guns and misunderstandings. Humans,new to traveling the cosmos,were in expansionist explorer mode. They were activating every dormant Mass Relay they found,and jumping to the other side,hoping to find new worlds to inhabit,new resources to exploit,and,just maybe,new life to encounter and become friends with. Or to go to war with,depending on disposition. Eventually,a Turian patrol fleet found a Human exploration fleet attempting to activate a dormant Relay. According to Citadel law,this may only be done with permission,given a VERY good reason,and under strict supervision. The Turians were informed that nobody had permission to turn on a Relay in this neck of space,so,they decided to uphold the law. By shooting down the ships. Surviving ships retreated to a nearby human colony,Shanxi,which was then razed by the Turians,who don't know what the word "Civilian" means,due to their culture mandating fifteen years of service to the state (Read: Military),starting at age fifteen. Humanity responded in their usual way: Come in,from one or two Relays away,with overwhelming force and take their property back. The Turians were surprised by this tactic,which is saying something for a military government,but what's more important is that they saw an unknown species attacking them,without attempts at communication. To them,this was war. Same goes for what the humans saw. Both sides knew little about the enemy. However,the Turians did have more ships,more troops,and better tech. When they began to deploy their fleets,the Council noticed,and intervened,brokering a treaty. It's a universally held truth that if the Council didn't intervene,the Human race would have been wiped out,or at the very least be made a vassal race to the Turians,but the Turians would have taken huge losses to do it. With this under their belts,Humanity began to make huge leaps and bounds in galactic society,solely because they had the balls to do what no one else did. The Turians are cold with them because of the conflict. Everyone else sees Humanity as getting too big for it's britches. Welcome to politics.
-The other races simply don't have the balls,power,or other things needed to advance their people in galactic society. Hell,by LAW,the Volus care not allowed to go above the Turians. The Volus are vassals to the Turian Hierarchy. Same goes for the Drell,who are vassals to the Hanar.
-The Batarians are a hostile state. When the Humans came on the scene,the Council pointed them to a largely untamed region of space,which happened to be the same neck of space the Batarian Hegemony was trying to develop. The Batarians protested this,claiming that the space was theirs. When they were brushed off (You don't have a claim on every world,four eyes),the Batarians withdrew from the Citadel,and began sponsoring pirate and slaver raids on Human operations in the Skyllian Verge,culminating in the Skyllian Blitz. The Vorcha,well... A Vorcha is lucky to live to thirty. Much like the Krogan,they evolved on a death world. Their natural life spans are criminally short,but they can,as INDIVIDUALS,evolve in the matter of WEEKS. As a result,they have a very warlike culture. Survival of the fittest,the strongest leads. As a result,they're largely incompatible with modern galactic society.
You're fighting to save galactic society because it includes YOU,and Humanity can't hope to stand on it's own.
Please,PLEASE,read your damn Codex. It answers all of your questions.