The entire design philosophy of the Epsilon is much more in keeping with how Federation ships should look. Also, it is a much more logical and solidly built hull. Whereas the Omega is spindly, fragile looking, and is only ahead because of Jupiter fanboys. #VoteAgainstOmega.
For my part, I find the Sigma hull to have better lines than the Omega, so that is where my vote is going. Also, the Omega's lack of a secondary hull that I can discern just doesn't jive with the way I feel Federation ships should look. But I can see from the way the votes are falling that my opinion is the minority.