I hated Bioware killing off the Geth with the Destroy option both because giving an entire faction varying dead/alive states makes sequels difficult, and because it felt tacked on just to make Synthesis more appealing. It was an example of the lead writers trying to nudge the players towards their favorite word baby. That the word baby in question was the most poorly conceived of three made it worse.
I felt the same. Why would the Destroy beam kill the Geth? The Control beam only alters the Reapers. The Synthesis beam is precise and sophisticated enough to change every single entity in the galaxy at the molecular level instantly and without visible side-effects except a spot of mind control (ugh, just writing that makes me wanna puke). Yet somehow, the Destroy beam's targeting system isn't sophisticated enough to distinguish between Reaper and Geth? That's some arbitrary BS only included to give Destroy a downside if you don't think of the Geth as toasters.
Anyway, I'll echo what some people said here, the trilogy had too many choices that ended up as genocidal dilemnas. It makes writing sequels more difficult when the PC decides the fate of entire species. Even had ME3's ending been well received enough not to warrant the serie's soft reboot in Andromeda, I have a very hard time seeing us play in a post-ME3 Milky Way where the Rachni, Krogan, Quarians, Hanar, and Geth can either be potentially exterminated, or enourmously crippled or empowered by the player's choices. in ME3 alone.
I actually think Dragon Age is way better at this. Sure, it had some weaknesses like Leliana being alive no matter what in DA2 and DAI, but its "who is king now?" or "which faction did you support?" style choices are usually more interesting and are better translatable into future games than Mass Effect's galaxy shattering decisions that are way above Shepard's paygrade and cannot realistically pan out in sequels unless EA doubles their budget overnight.
It is certainly a pitfall of the save import system. But I'm not certain if the alternative, to have canon choices decided for you in future games, is the better option.