I haven't used my flight sim in a bit but before I went to rotary wing flight school in the military I spent a lot of time with MS Flight Simulator and tweaking that rig for realistic flight dynamics in helicopters. The most important things are to have the controls setup to those on the actual aircraft, a large range of vision, and the aircraft flight dynamics file tweaked.
Flight Controls - I took a regular old joystick, removed the stick and made a new one out of PVC so that it would reach the floor. You will need to recalibrate the stick for the increased stick length but this is very easy. Since you're building motive skills that will need to be intuitive on the controls I believe that having controls that are in different places than real life or a pivot point on the stick that is much higher than normal will affect your skill transfer if that's your goal. Grab some pedals and make sure your throttle is positioned correctly relative to the real aircraft. All of this should cost you well under $300. Make sure your control parameters are tweaked in Flight Sim for realistic performance. Sometimes they're less sensitive which I believe makes it's harder to fly as well as less realistic.
Vision - I recommend the IR tracking system from TrackIR. It allowed me to use one monitor but still move my head around the cockpit and look around outside the aircraft when doing things like traffic patterns. You can even lean forward to look past a structural member. It's great software and much cleaner than having a wall of monitors.
Aircraft Flight Dynamics - You can go into the aircraft text files and edit their performance parameters. For helicopters this was particularly important as they were way dumbed down. I actually tweaked them to be slightly more difficult to fly and I was hovering an after market sim Bell 206 (DoDo Sim) after about 50 hours of practice at home. This transferred to hovering a real 206 on the first try at school without any prior real world experience which took about 10 hours on average for my classmates. If this level of realism can be done with a helicopter it can be done with a Super Cub.
As a side note, you can make flight sim as realistic as possible. In doing so it is a very powerful training tool that can allow you to practice. But your quality of training will only be as good as the environment you create in flight sim (wind, controls, etc) and how seriously you take your training.
Good Luck!
Josh