Here's my thoughts:
Technically speaking, assuming you have the Leviathan DLC, it would seem like a no brainer that the Defiance ending is the best. Flip off the star child, have some Leviathan's get your back (since they can also clue you in on the whole dealio with the crucible), save galaxy, profit. Of course it didn't work that way, so I got to work with what is actually there.
Destroy: I picked this first time through, and still stand by that this is the better of the four options. The geth may die (don't actually care about EDI) but it's morally the best ending. It's also the only one IMO that actually has you "win" in a sense, since everything else is sort of a sham in it's own way.
Defiance: The way it plays out it's a bad consequence, even though it doesn't have to be. I guess by all accounts it technically has the worst consequences, but I hold this as actually tying with Control for worse consequences.
Control: Let's assume for a moment that this isn't an indoctrination theory scenario (even though it totally is) The main problem with the control ending is thus: if we believe to a certain extent that the Hive Mind is exactly that, a Hive Mind, there's no reason to assume that the Sheppard personality will win out. For one thing, it's not just the entire Reaper collective they deal with, it's every single life form that was harvested up to that point. All of that buzzing around, and we're supposed to believe the Sheppard personality will keep the collective in check? Even though I don't believe in the hog-wash, the existence of several life, many of which probably stronger than Sheppard, being unable to take control shows that the Control ending is ultimately futile. By this ending's account, the process will simply start again, especially considering the Star Child's veiled threat that Sheppard WILL have to harvest at some point. By my account, we just watched the Universe's strongest warrior kill themselves as a means for the Reapers to trick sentient life (as they had done with the "Peace Negotiations" on Earth)
Synthesis: Despite the implications with the Control ending, I stand-by that the Synthesis ending is actually the worst one with the worst consequences. Again, assuming this isn't an indoctrination theory scenario (and again, it totally is) there is one major issue with the synthesis ending: it inherently destroys and will phase out all organic life. Let me explain: the stupid rational for the ending according to Star Child is that organic's lack the ability to understand machines and vice versa, and that giving both the opposite traits will create unity. First, how does giving a human robot parts suddenly make them synthetic friendly? After all, Sheppard is a hybrid themselves, and they can easily be anti-synth if needed. Also, how does giving a robot biological components suddenly make it like organics? Unless it's adding some sort of weird higher-brain function thing, I don't know how that'll work. But even aside from that, here is where this ending favors synthetics over organics. It seems the understanding of synthetics on an organic's part is all relative to that specific life rather than a mass wide problem in physiology. By contrast, we see first hand how machine life, regardless of type or form, can assess and incorporate organic traits into themselves. They don't become organic, but they can start to pick up and learn organic traits. What does this mean? Well, quite frankly, it's obvious that most of the change or "synthesis" that is occurring will target the organics as opposed to the synthetics. Changes will be made, but it's more kickstarting the aspects already there rather than making inherent changes to the system. In my mind, I see this leading to only to one conclusion: at some point, synthetics will eventually revert back to their original status since they are still the same entity essentially, and organics, what with their permanent change, will start to accommodate themselves otherwise, until all that's left is, you guessed it, synthetic. Plus, I just hate this ending on principle that it's all too "happy" and "peaceful" for my liking. Sorry, Commander Sheppard didn't get to where they were by be being some weird space-hippie.