I think you're underselling the organic/synthetic angle in ME1. Saren's entire spiel is about combining organics/synthetics; it's essentially a precursor argument for Synthesis. And, again, the first time you meet a Reaper, he makes it clear that the conflict between Reapers and the galaxy is about organics vs. synthetics.
Sovereign makes it clearl that the conflict is between Reapers and organics. It held the geth in contrmpt, remember. Not to mention the thorian, rachni, and tank-bred krogan we fought were all organic. AS well as Benexia's asari.
The Rachni Wars and the Krogan Rebellions also dwarfed the Morning Wars as far as destructiveness goes.
We were given to show the Reapers were a threat, yeah. But not synthetics in general. Organics were a far greater threat to themselves.
Besides EDI, Legion/the geth, Overlord, and the Reaper missions, you mean?
Clearly there are aspects of the ME universe that aren't directly about the organic/synthetic thing. That's inarguable, I think. But the Reaper plot is, and by extension the "main" plot of the ME trilogy.
Organic/synthetic relations as far as EDI go came to a head when Joker unshackled her. Otherwise it was her and Joker playing Odd Couple in the cockpit.
Overlord was dlc, and to me played more into a theme of man's inhumanity to man, what with the David angle.
Reaper missions? In ME2? Where? Aside from the Derelict Reaper mission and one or two Reaper artifact side missions, I don't recall Reapers playing a role at all outside of Harbinger's "asuming direct control"
Sure I'll grant you Legion. That's what, three conversatons and one mission. Clearly this dominated the entire trilogy 
Or maybe it was on equal footing with Mordin's talk of the genophage. Samara vs Morinth, and Jacob's missing father 