I've played a few hours so far and even though I love Gran Turismo, here are the first few things that stick out to me. 
 
Menu system - The menus seem poorly designed, VERY busy and badly organized. What they had in prologue seemed a better direction, this takes that but peppers the screen with other crap all over, it almost feels like i'm on a web site with a image map menu. Also, why is there STILL a million confirmations for everything? I want to buy a part for my car, 'are you sure' yes 'would you like to install this now?' yes 'part successfully installed' ok. Things like this become tedious when trying to upgrade your car or do other things, Ive been complaining about this in GT games as long as I can remember though, I just wish they'd do away with all that nonsense. 
 
Loading - It seems there is some kind of loading on everything you do, which get's very tiresome. Towards the end of my play today, I just quit to the XMB from the end of a race because I didnt want to have to sit through several different loading pauses trying to get back to the main menu. 
 
Graphics - While really nice, they are FAR below what I was expecting. It seems the majority of the unpleasantness comes from the shadows, they really stick out and look like first gen ps3 games did.  It may be my imagination, but I dont remember prologue having this issue.
 
I only listed my complaints. I really do love the game and the series however, GT5 so far is coming off as unpolished, which is the exact opposite of what I expect from a GT game.