I don't know CityVille but there are some information out there about the differences to Sim City 3000 (see quote and link below)
To summarize: You can't compare CityVille with Sim City 3000. CityVille aims for the causual gamer looking for an easy game with constant progress, more interactive elements, constant gifts and prices as rewards for doing somethin good and no chances to mess things up.
Not to mention, as a real mayor, you are not dictator and you can't truly pick out what buildings and businesses you want. Where are the bad neighborhoods in CityVille? Where are the strip clubs and businesses
you can't stop from coming in? In CityVille, everything is perfect and selected by the fuehrer, you. In SimCity 3000, you act like a real mayor and just decide what areas will be zoned as. This allows any business or residential complex to move in and set up shop.
There is also a constant barrage of "prizes" and "gifts" that you receive while working in CityVille. CityVille's basic strategy is similar to FarmVille and all those other Facebook games in that they just constantly give you prizes and encouragement for free in order to get your constant attention and possibly even your money. There is basically no way to fail in this CityVille game. In SimCity 3000, you can fail by losing money, letting your people be sucked up by aliens, or letting the city burn to the ground through disaster after disaster.
In CityVille, when you do something good, like completing the creation of a flower cart, you get points and coins and such. The aggravating part of this CityVille process is that you must click on everything to pick it up. As mayor in CityVille, shouldn't everything be brought to you? In SimCity 3000, there is no need to pick up rent or bonus points from every one of your city's buildings. These things are automatically distributed to you without having to take the time to do it and you then have more time to focus on building your city.
In conclusion, CityVille is nothing close to realistic and is a poor simulation to building a city. CityVille actually seems to be aimed towards the casual game player who was easily addicted to FarmVille. SimCity 3000 provides a much more realistic atmosphere and much more flexibility and less of the rush, goals, and rewards that make CityVille so tedious.