To answer the question froma different perspective I would say beyond the technical things noted by Overlord, there is absolutely nothing different about good v. evil.
Both cities will require the same things as far as quests, etc., althought he flavor of them will be different (In Qeynos: Go help so and so... In Freeport: Go kill so and so...)
The reason it has been so hard for me to play a toon in Freeport is that I like to roleplay. Roleplying bad guys means that you are acting evil, rude, mean, etc. all the time. Most players can only take so much, and everyone depends on others at times for groups and everything else. I just cannot see NBG, for example, in Freeport. It's all about greed there!
So until such time as SOE gives bonus xp to Qeynosians for doing good deeds and the same to Freeporters for doing evil ones, no big difference imho...