The Sophons (or as I call them in my mind after watching their intro, the Showpons), just seem abnormally smart. When you have major (and to a lesser extent, minor) races in the galaxy that are not so smart like the Cravers, or WAY too militarily-oriented like the Hissho and Yuusho, they seem... shall we say, a bit out of place. I consider intelligence a great gift, so the fact that there exists a race in the ES universe that is almost God-like in their intellectual superiority over the other major races is to me a (very) minor gripe. A gripe that is almost nonexistent after the inclusion of the tech-savvy Vaulters, but still there. 

That is a lore made for gameplay and immersion. They traded physical strength for knowledge. I do not know about god like intelligence tho, never went deep into sophons lore.

In my opinion, they are curious and don't really think of the potential ramifications of experiments like destroying Hekim's moon in a tectonics experiment

As I understand them, the Sophons aren't necessarily smarter than the rest of the factions. They just prioritize science and technology much more than any other faction, to the detriment of more basic things like economy and production. That's their balancing weakness. I don't see them as a God-like intelligence, or they would design better ships than we get in the game!

Personally I had the feeling as if the Sophone were designed earlier than some other races. They have a different "feel" and "tone" to them, and as such I agree that they (in a certain way) do not fit the galaxy that much with the other races in there. It is a bit too comedy in regards of immersion and epicness of the rest of the game.

I guess if you don't like them, just don't put them in your game :)

Not having fear of death should be a very complicated thing for mortals like us to understand the Sophons.