I prefer SC3k just because of the lack of a The Sims tie-in.
In 3000 you had the ability to get feedback from random citizens. In SC4, you had to import your own sims from The Sims 3 to get THE SAME DAMN FEEDBACK. If the feedback had been somehow changed based on your Sims' personality or something that would've been cool, but as it stands it's just a way to sell more copies of The Sims 3. Which isn't a bad gamme, but I should miss a feature of SC4 unless I go buy another, mostly unrelated game.
Oh and while the system wasn't as detailed, there is a traffic management system in SC3k. You can see which roads are heavily trafficked in one of the map overlays, then if you build other roads which are both close enough and parallel it'll reduce the traffic on the main road, and more importantly, it'll lower your road maintenance costs overall.
That was the nice thing about SC3k, really. It had everything SC4 did. It was just more subtle, less in your face. "Sure, I have quasi-realistic traffic modeling. But if you wanna focus on your power grid, that's cool. You're the mayor."