I am really not sure a player shouldn't progress in the wrong system, but if you take a guy like reggie bush and try to make him a power back, the cap on his strength, trucking, and other power type ratings will limit him. Also, there needs to be some sort of way to set up a training schedule. This way unless you put reggie in that system where he can thrive and train him in ways that can help him succeed he will never get any better. Also, if your coaches are more tuned toward power running he should never really develop as much because he isn't able to learn that system as well and will never thrive on it.
As far as this goes, a lot of this should come down to your system as well. I really hope they bring in the positional philosophies from head coach or something along those lines. If you are going to try to throw vertically a lot and have fast receivers then you might then you might be more inclined to go with a "strong arm/tools" QB and staffords potential in that system in might be very high. On the other hand if you have of receivers like marvin harrison or donald driver who don't really have that top speed but use their agility and route running ability to get open a lot or if you have a good defense and you are looking for a qb who can manage a game and not make mistakes then you would probably lean toward a "field general" type QB where sanchez being the more ready to step in, maybe having more accuracy and/or awareness and better intangebles will possibly be the better choice.
One thing that I will whole heartedly agree with you on is potential should be tough to reach. Even with great coaching, and everything done right it should not be a garuntee. I think with average NFL conditions and no interuptions for injury, in a system that is a good fit and being trained in the right way it should be something along the lines of this:
Player A has whatever rating of 55 and a potential of 95. There should be maybe a 1% chance that he hits 95 overall.
Maybe a 10% chance of reaching above a 90 overall. Maybe like a 15% chance of ever topping 85. A 25% chance of ever topping 80. A 45% chanch of topping 75. A 65% chance of topping 70. A 90% chanch of topping 65 and a pretty much garuntee of topping 60 at some point in his career.
On the other hand Player B has an overall of 70 but a potential around 85. This player is already ready to come in and start and could become a very good player but doesn't really have the hall of fame potential that player A had. Given the same "average NFL" situation he might have like a 10% chanch of hitting 85, a 45% chance of hitting 80, and be nearly garunteed to hit 75 at the height of his career. A much safer bet and more often than not the right choice but that 10% of the time that player A becomes an elite player he looks like the much better choice.
Obviously I took a pretty extreem example, especially with a guy like player A but that could be seen as a guy like Jerry Rice but taken kinda to an extreme with how he cam in. He was probably better than a 55 when he came in, I would have to say looking back around mid 60s with the streched ratings (average NFL starter) as he was a 1st round draft pick with multiple teams looking to draft him and had preformed very well at a small school in college. He also was decent early in his NFL career. Anyway doing this puts some risk on drafting the players who just have a lot of potential leading to it making sense sometimes to draft the safe pick.