I think Sims play a critical role in your training. But before I expand on that i have to say that is greatly depends on the type of device...not all FNPT are created equal..even though they may have the same certification level.
Having said that...IMHO a well developed training program should use the sim to introduce the training task and then you use the airplane to check whether you have actually learned the task. This is where we get back to capabilities of the sim...if its not capable of even flying straight and level or stabilized then obviously the device will not be as beneficial in your training.
Look at emergencies…how often to you practice V1 cuts in the airplane? Hope not too many… Decision making and scenario based training…there is a lot more to flying then knowing how to intercept the holding pattern. Sims are getting better but many times its like so many other things… Where can I find the cheapest FNPT?!? You get what you pay for!