Synthesis Pros:
Removes the synthetic vs organic problem
'Preserves' all of the currently existing factions (for a given definition of preserving after modifying)
Synthesis Cons:
Reapers survive
Non-consented mass modification of genetic code
Does not solve any problems not related to synthetic vs organic issue
Synthetic vs organic issue seems strained as no AI in game other than Reapers seems particularly aggressive or unwilling to cooperate
Control Pros:
Preserves all of the currently existing factions
Control Cons:
Reapers survive
Control Unknown:
Shepard playing God, which is extremely hypocritical after TIM
Destroy Pros:
Reapers destroyed
No external will is imposed on organic life and it's evolution
Shepard survives
Destroy Cons:
Geth and EDI destroyed
Synthetic vs Organic issue is not solved.
Personal opinion:
I find it strange that synthesis seems to be hinted as Paragon option. In ME2 Paragon Shepard reluctantly agrees to modify the Geth that followed Reapers as the only other option is destroying them. And yet somehow s/he would be willing to mass rewrite genetic code of every organic being when s/he does not NEED to?
I do not trust control. A ~30(?) year old human being turned into an AI through unknown means and then having to live through millennia while controlling the Reapers seems a bit ambitious. I have no idea if organics are ready for synthesis, but I have much bigger doubts about Shepard being ready to play God.
I went with Destroy, as it (under given circumstances) allows biggest amount of free will for all organic races. I also do not buy Catalyst's assertion that synthetics will always fight and defeat organics. There has been a grand total of one instance where that proved to be true - the destruction of Leviathan by Catalyst. Geth and quarians not only can make to co-exist, the Geth never posed a large enough threat to the galaxy as a whole to be an issue. All previous cycles were aborted thanks to Catalyst and Co, so this scenario never played through. Finally, if synthesis IS the necessary final step in organic vs synthetic debate, why do we need to force it through the will of a single human and an AI with slightly...unorthodox logic.
Also, what the hell IS synthesis? Is it a direct human-machine interface? IE something like what Shepard does with Legion through a tank, only without a tank? Ability to plug in technology in organic body? Catalyst claims that Shepard is part synthetic already, is he implying that any skeletal reinforcement/reconstruction makes you synthetic? So um...would human brain in synthetic body be synthesis? The description in game is just...completely unclear. I am having very hard time on seeing how modifying ones DNA could suddenly turn one into synthetic/organic hybrid. By that definition all GMO food has achieved synthesis, and Grunt is the epitome of Synthesis.