That's what space stations are for. Pretty sure there would be tons of people who even would prefer living in one rather than on a planet. Or else, terraforming.
Sure, you can go that route. That pales in comparison to having an actual planet to call home, though. Just ask the quarians who's entire civilization for the past few centuries has been living onboard space ships. Having a habitable planet is better than just having a space station.
And about the 1st paragraph....alert, indoctrinated presence detected

Doesn't take away from the validity of it, though. 
Yeah, I'm not sure why ME3 suddenly had a huge patch of galaxy called Alliance Space. Surely when they became a Council race it became Council space, and even if not it shouldn't have been nearly that big. That aside, I think it's said not even .1% of the galaxy has been explored by the time of ME1, which makes perfect sense. But if you think of it this way, what counts as territory isn't the billions of stars within, just a few key systems with Relays leading into the territory, if you know what I mean. The Alliance probably held more along the lines of 10 or so star systems.
Factor in the detail that the council has strict policies against activating relays. Humans didn't. It makes sense we 'discovered' and claimed a nice chunk of space outside our home. No other species was willing to explore those relays due to the council restrictions. The galaxy map could and likely is just a small portion of a much bigger connected system of relays. Imagine all the relays never activated, all the gateways to other regions of space that are just sitting out there doing nothing.
I can see political pressure being a cause of Alliance keeping that section of discovered space themselves rather than being absorbed into Council Space. Blame it on the turians. Lol.
Incorrect. This is a gross misconception that confused fans should really stop perpetuating because it only spreads more confusion. The reapers do NOT kill all organics. They harvest the advanced ones to preserve them in reaper form. Each reaper is a billion organic minds linked to form one gestalt consciousness. The memories and experiences of the species are forever preserved in immortal reaper bodies, ascending to new form of existence. The reaper's view this as preservation of life. It is not life as you know it but it is life never the less.
The multi-billion year old species that has been observing the galaxy (Leviathan) has noticed this pattern where organics create machines that in turn rebel against the creators. Organic life is wasted, extinguished. This pattern exists because immortal, practically god-tier organics have observed its pattern for eons. They created the intelligence which in turn observed this pattern for untold number of years (measured in millions, not our puny decades and centuries) and it too noticed the pattern. It's objective was to preserve life. It does this through the harvest through its definition of what classifies as life. Big shock that an AI doesn't view the organic body as a prerequisite for life.
It is wasn't only the billion+ year old reapers that have observed this pattern. It wasn't even just the EVEN OLDER multibillion year old Leviathans that observed this pattern. Even the protheans were able to discern the existence of a pattern. You may not like the pattern but in the fictional universe of Mass Effect it exists. It's as much part of the lore as the existence of mass relays. Nothing we see contradicts it. You can't view it relative to our petty, utterly insignificant timeline. The leviathan's and reapers are BILLIONS of years old. Their prespective on this pattern is not diminished by any of our limited observations. If anything, its proved. Even in our short existence as a cycle we can point to synthetic-organic conflict arising. The quarians are the perfect example, they're practically Mass Effect's version of Galatica.
If you'd like I could elaborate even more on this and help, hopefully, explain it to you. The reaper's are, imo, a immensely fascinating nemesis and don't get nearly as much credit as they should for their complexity. They're so much more as just these machines that kill people. That is a gross misunderstand on the reapers, one even Edi tried to smack you across the face about in the suicide mission.
the whole synthetics vs organics subplot being dragged into the reaper storyline
This would had been a valid complaint even if they went with the dark-energy twist. At least synthetic vs organic isn't something they pulled out their ass at the last moment. This is a consistent theme in the entire trilogy.
synthesis and control as options being asspulled out of nowhere
Synthesis I agree with. That ending is utterly nonsensical and I shudder to admit its existence. Control however? You think CONTROL is being asspulled out of nowhere? Did we play the same game? Control vs Destroy has been a reoccuring theme in the entire trilogy. Especially in relation to the reapers. Infact a good chunk of ME3 is spent with you talking/fighting Cerberus over CONTROLLING the reapers. Control was brought up from the very beginning of the game. Like, the first mission on mars introduces the concept and even shows the strives Cerberus has already made in their soldiers. We see the control ending gradually being escalated higher and higher. First with TIM's claims and arguments throughout the game and then with Horizon where we actually see the progress thats being achieved.
Synthesis definitely came out of no where, or at least the way it is portrayed in that ending. Control was there in the trilogy from day one with ME3 being the biggest advocate. If you seriously played through ME3 without noticing the constant foreshadowing for control, I don't know what to tell you. It's there, even if you didn't notice it, its objectively there. I find it surprising that there are people who didn't see it it, in all honesty. It's practically hammered home to you repeatedly. It was like it was jumping up and down in the background every 10 minutes going "FORESHADOWING FORESHADOWING FORESHADOWING!"
Theory: the Reapers we encounter early on did not explain their motives because they figured we were not capable of understanding them. Reality: most people do not understand their motives after explanation.
Theory fits evidence.
It's depressing how true this is. If Bioware did anything right with the ending its this. They said we wouldn't understand the reapers and clearly they were right, even when they go out of their way to explain it. It is all the more depressing that I genuinely don't believe people CAN'T understand it - its just that they don't want to. Many people seem to be so emotionally distraught by the ending that they latch on to ANYTHING that gives them more justification to hate it. It seems like they WANT to hate it.