If the argument is that Aeon is less played because it is weak (which is what your last sentence seems to be saying?) then you would expect Aeon to decrease in popularity as you increase in rating as faction differences matter more and more as ratings increase. However, you see the exact opposite trend for Aeon meaning that the faction pick rate has basically nothing to do with how strong the faction is at lower levels. Faction is basically never the reason you lost the game if you're under around 1500, some would extend it even higher. Maybe if you constantly play Seraphim v Cybran on Sludge you could have an argument.
Instead here are 3 reasons Cybran is more often picked than Aeon based on my reading of comments in casts and generic new player discussions:
- Cybran looks so cool
- Cybran has THE Russian waifu
- Cybran is sneaky and that's awesome