Synthesis is not a bad or immoral choice, though that is your opinion and I can respect that. Not everyone thinks that way. I see Synthesis as the way to propel the galaxy forward and out of the cycle that holds it back from true advancement of life. None of the choices in the end are easy to make, and that was the intention of the writers. If they didn't implement the "Geth and EDI will die" into the Destroy choice, then everyone would choose it.
Synthesis is the best way to preserve life in a form that creates equality between all species. It doesn't "homogenize" anything, because life still retains the organic genetic variation. It is also a natural endpoint to life in the galaxy (alluded to throughout the series): the Geth wish to reach a point where they feel equal to organics, and organics want a better way of life so they infuse themselves with synthetic material. You may say, "But they should be able to do that of their own free will!" and I would tend to agree, but given the scope of the war and the cyclic nature of the galaxy, I doubt life would get to that point before an organic extinction even occured.
It may seem immoral for some average joe to just say, "Hey, I'm gonna genetically molest everyone!", but if you put this in the context of the scope of the war and the immediate situation of the galaxy in the end of ME3 then it becomes more obvious (to me anyway) as the right choice. In either of the two other scenarios the cycle will continue to proceed unchecked, and life (organic life, anyway) will likely be exterminated. Why waste time trying to advance life to the natural endpoint of synthesis when you can simply get there and move on. Saying that synthesis will halt technological advancement is patently untrue, and if anything it will accelerate advancement at an unprecedented rate. The things that can be accomplished with the galaxy united (that includes the reapers, which are now equal partners in the galactic community) is unknowable, but will likely propel life into other galaxies in short order, and better to be a united front when we do so, because you don't know what is waiting for us there.
These are my thoughts in defense of Synthesis. You are more than welcome to not agree. That's why I love this game.
- Spiff