RE: Whats the difference.
I can whole heartily recommend the Avistar as that is the plane I am learning on. If you have the extra money, I would definitely take Mr67Stang's advice and go the ARF route. The radio that comes with the RTF version to me was rather "cheap". Of course this is to be expected. After only 6-8 weeks, I have already replaced mine. I of course just lucked onto a great deal, otherwise I planned to upgrade the radio when I upgrade my plane. If you belong to a club I would ask around, there is bound to be somebody that is looking to sell a 6 channel that would be great for this plane, as well as many more to come.
I also would suggest going with a better engine than the O.S. 40LA. It is adequate, and pulls the plane around nicely, but you can tell that it is bit sluggish. I don't know that I will ever be using this again, unless I am overpowering a 25 size plane.
Now the simulator question I can't answer for you...I bought RealFlight 3.5 right before I bought the plane. I was also originally looking at the Nexstar for the simulater, but it comes with an older version (2 I believe), and it only has the one plane. Purchasing the whole package allows me to practice more advanced maneuvers now that I have started moving past simple take offs and landings. Having this flexibility was worth the extra money for me. Since you already have a sim, I would suggest passing on the ones that come with one. You can always buy a new one later if you need the added features. Also once you have a decent transmitter you can buy one of the more inexpensive sims that don't come with a controller.
There is a also a really good trainer package, that comes with everything you need including flight line gear. It is from Thuder Tiger, Bigedmustafa (I think that is spelled right) has posted a review and links a couple times now. According to him it is very similar to the Avistar. You might search for his posts if he doesn't chime in on this.
No matter what, good luck. Any of the 3 choices you listed are great options, and you won't do wrong with them. Just make sure you get an instructor if you can. Even though you have some flight experience, flying glow engines is a whole new bag. There are a lot of things that you need to be aware of like engine tuning that flying electrics can't teach you.
Keep us updated on your decision and progress.