The lack of things in Broker, Bohan and especially Dukes.
I feel like the game really stressed you to be in either Algonquin or Alderney instead of in the other 3 boroughs. Lets take Beechwood City as an example; it's got a car wash, a cafe to play pool in and... nothing else. Not even a train station, really. Now AFAIK, there's so many different neighborhoods around that area and R* made it very small.
There are casinos (I don't know if it was pre-2008 though), strip clubs, one giant park, a large beach and a horse racetrack all in the area near Beechwood City. I think if R* put a new safehouse near Francis International Airport, they would have made the map a lot less concentrated in one area.
Another thing that bugs me is the train. Why cant we stand inside the train and look 3rd person instead of being forced into the train camera's viewpoint? I understand if it was to prevent idiots from making videos of 'gta IV massive train massacure hue hue hue' or something like that, but you can hijack a train in TBoGT and IMO that is just as bad.
TL;DR - A lot of the real city was cut and the trains suck.