Sort of stated my choice in my 2cts post I just put up, but found this thread highly interesting so I'll try and put my choice into words. I'll be loaning some arguments from earlier posts though as I happen to agree with them.
Control
I think as a Paragon player you can't choose this as basically you would sort of be a god and decide the evolution of the galaxy on your own. Imho, this is outside of Shepards character who is about letting people decide for themselves. For good, or bad. Also this option feels really awkward to me. There you have the reapers, destroyers of countless civilizations and murderers of countless of souls, not to mention the trillions that died in this latest reiteration of the cycle and now we have them roam around like nothing happened?
It would be like defeating Nazi Germany and then letting Hitler, Goering walk free saying as they would say, we have a new leader so all is good now, you can trust us. I simply cannot see it work. As long as the Reapers remain I think most if not all people would NEVER feel save. I suppose one could argue that Sheplyst could make the reapers fall into the nearest black hole, but if he would do that he might as well pick the Destruction option as the result would be the same and as a bonus he would survive.
I would feel a little bad about EDI and the Geth, but I think if given the choice they would sacrifice them for the greater good. Also I wonder if the Geth are still considered synthetic or is having a soul the distinct qualification for life? If the Geth are considered to be alive then the crucible should spare them (that would leave poor EDI (and Joker)). If not, I see nothing that would stop anyone from creating EDI and the Geth again. Granted, both are not simply created but even more so a result of their experiences, but it should be possible to (at least in some extent) to duplicate those experiences and recreate them to the state they were just before the crucible fired.
As a side remark. I haven't got any DLC for ME3, but reading through this thread I read up on the Leviathan one and I might buy this one after all, but for me this is another reason that the Control option is out of the question, because if I read it right the Reapers are actually a VI creation by them which rebelled against them. If one Godlike race failed to foresee their own creation turn against them who is to say it wouldn't happen again with Sheplyst at the helm?
In fact one could also argue that it still would be possible that at some point organics and synthetics will be at each others throats again. After all, Sheplyst only controls the reapers and who knows what synthetics will be created in the future? What would he do then? Whose side would he take? Might it be possible that he comes to conclusion that the harvest is necessary after all? Or should he have chosen for Synthesis after all?
No, all things considered Control is out of the question.
Synthesis
The " Everybody needs to be happy" option and while I do like happy endings overall I felt that this was a cop out. Also again I feel that Shepard would essentially act like god which is outside of his character. This whole synthesis tasted to much like the borg mantra "We will add your biological and technological distinctiveness to our own". Mordokai called it rape, and that's exactly what it is.
While in my view of Shepard he will do what needs to be done to defeat the reapers it's an entirely other thing to just merge organics and synthetics. The whole saga was about defeating the reapers, forcing the entire galaxy to some kind of mind/body-meld was not the plan so no. My Shepard will allow the galaxy to make it's own mistakes and if that means that organics will be wiped out and that's on the head of a future generation.
Also the catalyst self said that Synthesis was inevitable. Well, if that's the case I see no reason to hurry. It will come when the time is right and my Shepard will be damned if he forces it on the Galaxy.
Destruction
Imho, the ONLY right choice. When you have the opportunity to end a threat that threatens every advanced civilization in the Galaxy with annihilation, a threat that has annihilated countless civilizations in the past then you END that threat. And while the other 2 endings also will end this threat they both (the refuse option I refuse to discuss (pun intended)) have to much downside to be considered.
And if the Catalyst is right, and he probably is since he is way more intelligent, Synthesis will happen eventually anyway and if that's the case there is no reason to let it come naturally instead of forcing it down everyone's throat.
Of course this option also had the added bonus of Shepard surviving and finally be able to settle down with his love.