I'd argue that organics vs synthetics is much more fitting to ME universe as a whole (and ME2 in particular) than dark energy. Legion's loyalty mission and his character, Overlord DLC, Rogue VI hacking mechs, Tali/Legion confrontation all touched the subject. As for dark energy, it was mentioned by Veetor, Tali and Reegar regarding Haestrom mission and probably 1-2 more times (don't remember, might be none at all) but there was only one quest focused on that idea - Tali's recruitment. While there are three focused on organic vs synthetic theme.
If you look at ME2 and ME3, the organic vs synthetic theme is present in both, while dark energy only gets introduced in ME2. I think they made the right choice to go with the organic vs synthetic theme in ME3.
And tbh, I think ME2's disconnection from ME1 attributed to several flaws in ME3 writing. The writers were forced to tie together the loose ends and did not manage to do it completely (purely due to time constraints IMO). Still, I think they did a great job with the limited time they had.
Well it's not just Dark Energy itself,like you mentioned, is only exposed during Talis mission, but the genetic diversity of humans which is very prelevant through out the game which is why the Collectors harvested them which is an important plot point to the whole dark energy mumbo jumbo.
While the organics vs synthetics theme absolutely is there and is an important part, but it's a reoccuring theme, it never comes of as something part of the grand plot since, it's not part of the main mission while Dark Energy is(The Reapers use genetic code to solve the dark energy problem, humans are unique in their diversity and beacuse of this get targeted by the Collectors to find "the sollution")
But i agree with you that the problems in ME3 started in ME2 or even earlier, i'm not so much critezing ME3's writing, overall, i acually think it's story telling, pacing and dialogue is the best in the series. Where the other 2 games made me decide who or what lives or dies, ME3 made me wonder what makes a person and whether or not i could consider a robot alive, and the organics vs synthetics theme is familiar enough for the ending to sort of work even if it might have not been fantastic.
I'm more critizezing them for not writing a more cohesive trilogy. They knew what it should consist of but they didn't really seem to be able to decide how to put it together and made it up as they went along.
I feel that since the Collector/human genetics/dark energy plot shouldn't have been simply abandoned. Maby it wouldn've have been better to never introduced it at all and had "man vs machine" take a bigger part in ME2's plot(hell i'm surprised they didn't since Shepard is half synthetic at that point), but since they did i think they should've built on it.