A 46 megapixel FF camera will have the same pixel density as an 18 megapixel APS-C camera.
The most critical limitation on the camera will be the glass used. On an APS-C camera, if you want a sharp picture you have to use top-of-the-line lenses, the sharpest lenses that canon offers. Use anything else and image quality suffers.... perhaps this is why there has been so much effort updating Canon Lglass.... so that when a high megapixel camera comes out, it can have glass that works with it. (Are you listening Nikon?)
The second limitation is caused by the smaller area of the pixels. You can expect the same IQ as that of any of the APS-C cameras, unless the release of this new camera is coupled with newer and better sensor technology.
I do not believe the doom and gloom predictions of slow frame rate because of a larger sensor. The time spent reading a sensor is small enough to be ignored.... time spent processing the data and storing the data onto a memory card are the big killers.... but one can increase the buffer memory enough to allow a string of several dozen pictures to be taken at a high frame rate... and the speed of compact flashes is steadily going up... you can now get ones that write at 145MB/second. I have some 4X speed (600KB/s) 1MB cards.... It has come a long way since then and I will be very surprised if we do not soon see 2000X speeds. Likewise, we now have Digic6. How long before we see dual Digic6... or even quad or hex?
. A data processing/storage system able to handle files twice the size is not a big jump.... After all, the world did not end when cameras jumped from 10Mpixels to 18...