There are multiple zoom levels, 100%, 75%, 50% etc. On my 1920x1080 monitor at 75% it’s pretty darn close to my real iPad 4 (same screen as the iPad 3). If I drag my simulator to my 13" MBP, I keep the same relative size and it’s still a pretty close match for my real device.
Of course your monitor size is going to control this. I have a 24" monitor that has to fit 1920x1080 pixels in it. If your on a 20" monitor at the same resolution, the simulator will be smaller. If you’re on a nice big 27" those pixels get spread out more and the window will be larger. There is no way we can accommodate every possible monitor size at a given resolution.
I believe previously, it probably defaulted to a zoom size that fit the screen better, and now it defaults to a size that gets the whole skin on the screen (I’m not sure about it, since it remembers your zoom settings from skin to skin and I’ve switched around so much).
Rob