I can imagine Shepard by the crucible about to make his choice when he manages to ring up every race in the galaxy to ask for their opinion.
Shepard: "hey guys! so i met the reapers master and he's giving me three choices to end this war, check em out!"
"So the first lets me become an AI and will give me complete control of the reapers and I will be able to do whatever I want with the most powerful force in the galaxy and I'll prreeeeetty much be a God deciding who lives and dies, I swear I'll use it for good!...and everyone lives (for the foreseeable future)"
Rest of the galaxy: "Yeeeeeeah, I'm not sure if I'm entirely comfortable with you having that much power, and our lives hanging by your every decision"
Shepard: "Okay guyz, that's fair enough. How about this one? It says I can destroy all the reapers!"
Rest of galaxy: "OOOHHHH that sounds good, do it do it do it!"
Shepard: "BUT it'll kill the geth and edi and the virtual aliens and any and all other synthetic life forms"
Geth: "WOAH WOAH WOAH! Slow down there Shep, we really would prefer it if we didn't have to die, I mean we're working with organics for like the first time ever and now you all want to kill us? WTF?"
Shepard: "okay, i see where you are coming from geth friends. This last one is called Synthesis, and it gets pretty good, check it out"
"So all organics will now be able to fully integrate with synthetic technology, which means you all can like play video games in your mind and stuff, and directly connect your consciousness to all other life in the galaxy"
"Hey krogan! Remember when I sabotaged the genophage cure?! No? Oh well, if I choose this option then you won't have to worry about it at all because this will pretty much eliminate every disease from every organic. And krogan, you'll have access to a vast array of previously unavailable knowledge to rebuild your once great civilization"
Krogan: "Hmmm, no more genophage sounds like a pretty good deal..."
Shepard: "Salarians! You know how y'all are crazy smart?!?! Well, you're just about to get WAAAAAYYY smarter, and forget your short life spans, you can pretty much live forever know if u want"
"Liara! Remember how you loved learning about about the Protheans?! Well guess what? Now you'll have access to the knowledge of EVERY civilization that came before them!"
Liara and the Asari: "Hey that sounds pretty sweet"
Shepard: "Geth! Edi! This one will let you have a full understanding of what it is to be an organic! Just like you guys always wanted! You know, EDI with all your questions about hooking up with Joker and understanding what makes organics tick, well now you'll know exactly!"
"And those cute Geth and Legion, always watching us from afar desperately trying to understand how to approach us without having everyone want to kill you! Worry no more! And best of all guys: YOU WON'T DIE!"
"Quarians! You know those pesky immune systems you guys are always worrying about? BAM! GONE! You'll be free to live wherever you want with or without a suit. And you'll forever reunited with your children, the Geth!"
Quarians: "Keelah se'lai"
"Reapers! All you tormented souls in anguish in Reaper form, well now you'll be free from your eternal hell!!!"
"As a plus everyone's DNA and coding will be augmented with an entirely new framework, but don't worry nothing is getting removed! You all will still be you, with complete memories and experiences and perception, intact and unchanged. Everyone is just "augmented" so to speak"
"So everybody! what do you all think? Of course I could always reject all these options and we can all suffer a slow, painful, agonizing death at the hands/claws/tentacles of the Reapers, with all that in mind what do you all say?"