The Rachni and the krogans are known quantities, the galaxy fought them and won. And you have Javik as an independant source that the Rachni were screwed over several times to fight wrs, they actually have tno interest in. The Krogans are demilitarized completely and their superior number amount to nothing if they can´t build a warfleet. Also they are part of the galactic community for nearly 2000 years.
But well, it´s not like everyone here cures the genophage or releases the queen. The difference is that the game talks about the genophage and the rachni from day one more or less and you have a lot more info about the situation than this whole "hey, reapers aren´t genocidal maniacs, we have good reasons and evidence we never show." And the Catalyst isn´t evil, because, it was programmed to do so. Yeah, that´s nice, we shut down faulty machines that are a safety hazard. the player got enough information to decide yes/no when asked about the Rachni/Geophage thing.
The Reapers have superior numbers and technology and shown the willingness to genocide everyone, believing that they save them by storing them in Reaper form. And this whole storage system is a big unknown. As far as we know, the particular species in storage is more or less dead and they just ripped the knowledge. There is a (gestalt?) central intelligence and every Reaper bought into their agenda completely, using the same mehods, spouting the same nonsense. And well each one bows to the new master.
This "emotional manipulation" didn´t start in ME 2. Husks appeared long before Sovereign made his speech, indoctrination´s effects were shown before as well and Sovereign was a condescending arrogant jerk and this whole "we do it for your own good" only appeared in ME3 or ok, Harbinger´s last speech in ME 2. And well Saren told us that Sovereign despised his own allies.
Sorry that I don´t buy into the poor misunderstood Reapers thing, when everything the Reapers ever used was made to subjugate, destroy and process either into reaper form, as indoctrinated sleeper or as cannon fodder on the battlefield. You had no own will in reaper or husk form and they never bothered to ask if you want their awesome form of ascension or if you are interested in volunatarily working towards synthesis. They just popped up, controlled and killed everyone and made a new reaper out of organic paste.
You don´t need to slap an "evil" tag on them or being manipulated by abonimation aesthetics, to rationalize that you don´t want to be good neighbors with the dudes who made it a bllion year old habit to come out of dark space, guns blazing, only stopping after every member of every spacefaring civilization is dead and who only deigns to acknowledge you, when they are unable to kill you, yet.