I currently use FS2000 and am very happy with it (although I have no experience with Fly).
May I suggest to you another sim you may not of heard of. It is called Airline Simlator 2 and in my opinion is a superb sim. Although the visuals are quite basic the handling and systems on the aircraft are amazing. It far surpasses FS2000 on reality as far as systems goes on the aircraft. It includes a fully functional FMC and EFIS on the 747-400 and you can also fly with ATC. Make a visit to
www.rcsimulations.com and find out more if your interested.