We can talk about three basic types of controllers for flight simulators: simple single-piece joysticks, dual-piece HOTAS (Hands On Throttle And Stick) devices, and yokes.
The latter category can be recommended to gamers who prefer peaceful flights on heavy aircraft in games like Microsoft Flight Simulator or to bomber pilots in combat-oriented games. Yokes make it more realistic to control airliners and other heavy aircraft. However, they are not so good for controlling a fighter because it's hard to perform sudden pitch change maneuvers due to the yoke's excessive resistance when you're pulling or pushing it. Besides, there is little choice in this device category. I can only think of such products as the Saitek Pro Flight Yoke System and a couple of devices from HC Products: Flight Sim Yoke and Eclipse Yoke (the latter is perhaps the only new product for the mass market CH has released in the last decade).
Thus, we are left with two types of joysticks that have a classic control stick. The HOTAS design with separate control stick and throttle units seems to be only justifiable for products which are above the average in quality and price. They offer a lot of axes and buttons and may seem to be too complex for a user who's not used to flight sims. As for inexpensive HOTAS devices such as the SpeedLink Black Widow and Thrustmaster T.Flight Hotas X, their functionality is comparable to that of a regular single-piece joystick and they do not allow you to control the aircraft without getting your hands off the joystick, which is the point of the whole HOTAS concept. You have to use your keyboard to perform secondary functions.
Well, you can’t really do without the keyboard’s help even if you’ve got a top-class HOTAS system when you want to play a truly lifelike sim of a modern fighter in which the list of control options takes a few pages in the user manual. Still, you will have to take your hand off such a top-class HOTAS less often because all frequently accessed options can be assigned to the joystick's buttons and axes.
So, I guess that a user who's new to this whole flight sim business would be on the safe side by preferring a regular single-piece joystick as his first device since it is going to be more versatile than a yoke and much cheaper than a full-featured HOTAS system. But if money isn't a problem, a HOTAS system would be much more attractive.