Personally, I think the Reaper's solution is, while it is the best from a logical standpoint, I don't see it as the best overall.
People have already discussed the whole Quarian-Geth controversy, and how it in turn shows that there can be, in fact, Organic-Synthetic coexistance. In fact, one of my many gripes with the ending is that this theme that's heavily explored (and is ultimately the best end for the Quarians and Geth) in ME3 is utterly thrown out the window in Mass Effect 3's ending.
But even disregarding that, going on the Reaper's side of experience and believing them when they've said that they've seen Synthetics nearly destroy Organics and thus killing all of them will prevent the end of all life, I still think this theme is crap for both one of Mass Effect's other main themes and a very recurring theme that I hold a bit dear to me.
Mainly, sometimes the logical decision can go suck it.
The Omega 4 Relay? Tempering the horrendous race relations between the Salarians and Krogans? Or between the Quarians and Geth? Exploring most of these options logically, most people would tell you that pursuing such actions would be near-suicidal, and not worth the risk of exploring. This theme is also evident in many other fictional media, such as Puella Magi Madoka Magica and Tengen Toppa Gurren Lagann (and anyone who's a fan of the latter is probably drawing so many comparisons between the Reapers and the Anti-Spirals that you're wondering if one of the writers of ME just finished watching TTGL and thought to make the Reapers into those things), as well as a few ventures into real-life itself (*cough*MoonLandingTranscontinentalRailroadRacialEquality*cough*).
We, as a species, pride ourselves on building off of the impossible and proving that we can defy all odds and do something that many others have already wrote off as, not only impossible, but completely fucking insane. Hell, Shepard's pretty much done the exact same as before in his fight against the Collectors and Saren before them, so I don't see why, in the face of all of these odds, he simply doesn't turn to the Catalyst and say "Screw you."
Especially when this is a very popular theme for many fanfiction writers who have explored alternate endings to Mass Effect 3's [http://arkis.deviantart.com/art/Mass-Effect-3-Alternate-Endings-SPOILERS-289902125]. Shepard has, for the past three games, been building up everything for the final, inevitable battle against the Reapers. As many others have said before, there should be an option to sit your ass with the Catalyst, stare out the window, and see whether or not all of your efforts, uniting the galaxy through three games worth of continued continuity, several hours of addicting Multiplayer, will result in the galaxy defeating the Reapers.
And even if it didn't? Fuck, imo, that'd still be a more appropriate ending than what we got. I would bet all of the credits in the Milky Way that you could ask every single Squadmate you ever got in Mass Effect whether they'd want to go out fighting against the Reapers or have everything they've worked for completely trashed in the cop-out endings, and they'd all agree they'd rather take Harbinger's beam to the face.