I like the "red side" quite a bit. At the time that City of Villains was released, it was my favorite side, and remained so until I stopped playing (I think I drifted away right before "Going Rogue" went live. At least, I don't remember making a Praetorian character until Homecoming).
I always thought that the twisty, garbage-strewn, back alley and claustrophobic feel of the Rogue Isles was more "realistic" than the comparatively neat and orderly ninety degrees grid layout of the city zones in Paragon City. (There are spectacular exceptions to this, but I mean the Galaxy City>King's Row>Steel Canyon zones that most of my Heroes got very familiar with. Also, I really liked how you could see every stereotypical Dilbertesque "No one of us is as dumb as all of us" corrupt ruling party trope in how the structures in the Rogue Isles are piled up on top of each other. One look at how the Arachnos bases are just stabbed into the landscape with their weird sections of catwalks and walls and you know that you are in a place where environmental concerns are ignored and unfettered mad science is the norm. It looks different and cool and the same as where you live, except now you have superpowers. Of course you don't mind robbing a bank for a guy who hangs out on the docks. Wheee!
Anyway, I think the Rogue Isles aren't designed to be universally appealing. I think they are a work of art designed to feel like a place where villains are in control. And one of the things about art is that not everyone likes it.
Well, it isn't "just" a city with Villains in it. Arachnos is everywhere in the Rogue Isles because Lord Recluse isn't just a powerful Villain, he's the Ruler, the The Guy in Charge of the Biggest Gang™