I think there is an issue with virtual controls in that you often (but not always) have to look at the controls before you know where to press. Gyro controls also move the image you are looking at, which makes racing games a bit annoying - that's why developers have to counter the movement to keep the horizon level with your eyes.
Another issue is that the controls are mostly used just by your thumbs as you are holding the device. This is very limiting as you only get two simultaneous inputs. Then there's the problem of your thumbs covering up what you are looking at.
As for the controller design, I don't think it would be good to follow the common controller designs because there's no point in designing a sleek, compact iPad and have you carry around a huge, awkwardly shaped controller like the 360 controller just to play games.
I think they just need to build a compact touch slate. I've used this image a few times now but I think it's a solution that would work in many scenarios, even beyond gaming:
This would be perfectly flat with 3 segmented touch pads with a glass surface. Likely smaller than the picture too. Because it's flat, it can slip into one of the bars of the smart cover.
If they are really clever, they could find a way to charge it while it's in the smart cover from the iPad battery but I suspect that would over complicate things.
The pad could have the standard gyro/accelerometer controls. The lines in the pad can be superficial to separate the main controls. It won't give the same number of independent controls as a 360 controller but with the possibility of gestures, it offers enough controls.
The best thing is that it can double up as a remote for controlling the iPad via Airplay. Because it has no integrated display, that should help keep the cost down so that more than one can be bought and it means the battery lasts longer.
The shape also means that it's easy to take over to a friend's house in your pocket for multiplayer Real Racing via Airplay using a single iPad.