The Krogan hold the galaxy hostage until their cure is ready, despite knowing that everyone will die if the Reapers win. In fairness, it probably was their only opportunity at ever getting a cure and they were going to die either way if they didn't.
I don't really buy that. Wrex says that only by curing the Genophage will he be able to unite his people ME 3, but that goes completely contrary to what he said in ME 2. In the second game, he says that the only way that clan Urdnot was in power was because he was able to leverage control of the viable females.
If the Genophage is cured, then all that power structure is gone. Why should the other clans listen to Wrex if they have their own fertile females to bargain with? Why would a Krogan warlord even bother with the alliance with the galaxy once his females have been restored? One might say that Krogan clans going against the alliance is stupid, but Wrex was perfectly willing to go to war with Humanity in the middle of the Reaper invasion when he discovers the cure has been sabotaged so it's not like that sentiment is unfounded.
Putting a full stop to the war so that the Genophage can be cured, is no way to garner allies or goodwill. Holding the galaxy at gunpoint, causing the deaths of millions of people a day, because of some 2,000 year old grudge is moronic, and the narrative doesn't even let the player call Wrex/Wreave out on it. Working with the galaxy, having 'the Shepard' put in a good word to the Council races, etc would have been far more effective, and could have potentially even brought the Salarians around in support of the cure.
I don't particularly care for hypocrites or bullies, and the Krogan are both throughout the trilogy, especially in the third game (IMO).
The geth acknowledge the threat and pledge to help, but subsequently spend their time building a useless Dyson sphere which gets blown up by the quarians, then they actually go and ally with the damn Reapers.
Yeah, the Geth's actions between ME 2 & 3 have me scratching my head. Legion says that the Geth will aid Shepard in the fight against the Reapers, but it also says that the Geth are building a structure so that 'No Geth will ever be alone'.
A Dyson sphere is an immobile ball surrounding a star; forgetting the impracticability it would be to actually build one around a main sequence star like Rannoch's sun, or the irreparable damage that blocking out the light and heat would do to Rannoch itself, what did the Geth actually hope to accomplish with their grand project? A Dyson sphere can't move, and by the way Legion was talking every single Geth program was going to upload to it, meaning that there would be nothing left to control the various platforms or ships that it promised us in ME 2; sounds more like the Geth were planning on hiding than anything.
Unless their construct was going to be armed with the destructive firepower of entire Reaper fleets I don't see how it in anyway could have helped contribute to the fight.
The quarians acknowledge the threat and pledge to help, but then send their shiny newly armed fleet against the geth instead. In fairness, they wanted a place to offload their civilians so their ships could actually be useful in the fight, and Rannoch's the only place that would work for that.
The Quarians' decision makes more sense than the Geth's, but all the secrecy and lone wolf tactics was their major problem (IMO). The Admiralty should have told the other species what they were planning. Even if Shepard was unable to convince the Council to send aid, at least the galaxy would have known that the Quarians weren't abandoning them to die while they flew away in their Migrant Fleet.
If the player sides with the Quarians, he/she has to spend time after Rannoch trying to smooth over relations between them and the rest of the galaxy (the interview with Diana Allers, etc.). Not as much as the Geth obviously, but enough time and effort that could have been used for something else if their leadership had just been upfront about the whole thing.
At least the Quarians made a choice that was reasonable, they didn't try and hide from the Reapers like the Geth or Leviathans, nor did they try and hold the galaxy hostage to try and get concessions out of the other species like the Krogan.
Batarians get predictably annihilated offscreen for being a comical isolationist pariah state.
It would have been nice to actually see the Batarians in a light that wasn't racist, slaver, jerk-hole for the entire trilogy, though the fall of Karshan at least made sense in terms of the established lore. Indoctrinated high ranking officials throwing the military into disarray just as the Reapers invaded; cold and effective, a perfect example of the dangers posed by Reaper influence.
Leviathan sit in their goddamn ocean trench until someone comes along to tell them what a bunch of idiots they are for creating the whole mess by being the worst AI programmers in the universe.
Very true, their whole reasoning behind the creation of the Catalyst was face/palm inducing, but the survivors' actions in hiding from the Reapers every cycle had worked just fine up until this point. I can at least understand their inaction from that perspective. "If something's not broke, why try and fix it?"
Only the Rachni really commit and then don't do anything but prepare, but they get destroyed and their queen enslaved offscreen.
The Rachni are the only species to wholeheartedly agree to aid Shepard throughout the trilogy, and they are thanked even less for their help than the Asari or Krogan, who both actively derailed the galaxy's efforts to defeat the Reapers.

The narrative railroading that saw them wiped out off camera is mind numbingly moronic (IMO) compared to what we are shown of them in the first two games.
We are supposed to believe that a species who knew of the threat posed by the Reapers and devoted themselves to stopping them, a species that had survived two galactic wide attempts at genocide (the Protheans, and the Council), a species that had started with one Queen and two years later was executing rescue operations with Rachni built spacecraft, a species that could survive on some of the most hostile planets of the galaxy, far out of sight from any prying eyes, a species that is capable of producing combat capable soldiers in a matter of weeks and has been doing nothing but that for over two years (if the player spared the Queen) is completely taken out and utterly defeated before the third game even begins?
That doesn't make sense, the Queen was smart, she knew that avoiding detection until the galaxy was ready to fight back was the best method of survival all the way back in ME 1, I don't see how she could have been discovered so easily when she took great pains to ensure her secrecy. The only way I can justify that writer fiat is if the Reapers knew the threat posed by the Rachni. How they over any other species in the galaxy; even Mary Sue humans; needed to be taken out first and they sent their entire armada scouring systems until they located the Rachni and overwhelmed them with sheer numbers.