I can sort of envision an inversion of the final ending choice, where you can have TIM survive against Anderson and have him only able to enact Destroy, while you choose Control and put him in a position to enact your will or even use him as your physical avatar.
So... you grab the rods and upload yourself into the Reapers... while TIM blows the whole system sky-high? 
Conversely, Anderson would be able to enact Control, if you convince him that his idealism and strength can be used to change the Reapers to benefit the galaxy in a good way. And he could also enact Destroy. Meanwhile, you could enact the Control that TIM wanted, so there'd really be no difference there.
I don't get it. Why have them at all, if they can choose or be persuaded to choose any of the options you can? Because they're there? If so, anyone can be persuaded to do it, in which case we're back to the question of who'd you put in your place.
That said, I don't really know why you wouldn't want TIM in control of the Reapers. What would he do that disgusts you so much? I mean, if I had it my way, destroy really would be the only viable ending, with the others being faustian deals that really do nothing but enhance the power or ideals of the Reapers to have them permanently enact their solution. I'd do it as a showing of what would happen if you trust the Reapers.
And as I said, that's exactly what I was calling for as well. More understanding and substance to what each ending really is, and what each ending really does. Looking at it, looking at the history of the Reapers, looking at the logic and the reasoning behind the problem the Reapers are trying to solve, looking at the history of the galaxy and the Leviathans history, I came to a conclusion that Destroy really truly was the only acceptable option. And I'm saying this as the guy who doesn't hate the Reapers as they're made out to be in ME3. I'd rather they were something more along the lines of what I made them out to be, but the ones that we get aren't ones I can really despise, though also not ones I can allow to exist.
See my opinion of TIM for your answer. Though, if I were fully consistent with my views of control, a TIM control entity would grow disconnected and abandon the piddly organics just as easily as any other. But I wouldn't be willing to put up with him until he did.
I agree that controlling the Reapers is not an ending I expected and synthesis is downright batshit lunacy. But I can see the, presumably "original intent" behind having them, namely providing different kinds of victory. You can get your basic, good guys win, bad guys lose (and as always England Prevails) victory (destroy), you can get a personal ascension to nigh-godhood victory (control) or a "make the galaxy a better place" victory (synthesis). The problem isn't with the choices themselves, it's the **** sandwich they're wrapped in, particularly the latter. To that end I wouldn't want to just invalidate two of them. Yes they're unexpected but with a little prerequisite work they could've been made to fit.