Isn't this because the GPS on the iPhone is assisted and not true?
Unfortunately, if you are using non-assisted GPS on these newer phones, you get poor performance. They were designed for AGPS and lack the necessary hardware that dedicated GPS units use.
Poor performance meaning usually very long acquisition time and less accurate reception (unable to handle many satellites, etc.)
There is a comment above on Apple choosing a lower sampling rate in exchange for better battery life. I think this is probably right on. Most users will only be using the GPS to mark driving directions or to record something like running. In these cases the GPS is definitely good enough (you're just hugging streets anyway). Unfortunately, it's not good enough for me : ).
I would definitely be more than willing to run more tests or try different programs if people throw out ideas.
By way of another example, their approach to being caught with their hands in the signal cookie jar with regards to the iPhone 4 signal problems (specifically, how they manipulated the bar calculation algorithms to show a stronger connection than other devices for a given signal level)? No worries, we'll fix that, but we'll make bars 1-3 taller so that psychologically, you feel like your signal is better. Apple is masterful at manipulating what people see to get them to believe that they're getting the best possible experience, but the laws of physics dictate that they have to cheat somewhere sometimes. I don't mean that to sound perjorative, but just to point out that part of Apple's ability to do user experience so well is their ability to manipulate the user into thinking the positive things they want them to.