Given sensors of equal pixel density and quality I'd rather have more of the image circle to work with (and a bigger viewfinder) and crop as needed. IMHO this "advantage" is a case of camera makers convincing buyers that its lemons are really lemonade.
Of course you would, and so would I. When full frame 35mm cameras reach the pixel density of the cropped format cameras, there's absolutely no image quality advantage in respect of one's longest telephoto lens, with the cropped format. The only advantage, as Pegelli mentions, is the lower cost and weight of the cropped format.
However, Canon FF sensors are always
behind the cropped format in terms of pixel density. The 1Ds2 has the same pixel density as the 6 year old 6mp D60, and the 1Ds3 and 5D2 have the pixel density of the 4 year old 20D. The 50D has almost double the pixel count of the 20D. For a full frame sensor to match the pixel density of the 50D, it would need 39mp, the pixel count of the P45+.
The other issue is edge performance. All 35mm lenses have noticeably worse performance at the edges of the 35mm full frame. The Canon 100-400 IS has much better edge performance on a cropped format camera. However, even on a cropped format, there can be noticeable resolution fall-off in the corners.
Recorded image resolution is always a combination of sensor resolution and lens resolution. If you increase either one, you inevitably increase image resolution, by at least some degree. Whether or not that increased resolution is noticeable on a print of a particular size, is another issue.
Sensor resolution is limited by its pixel count. There's a fairly sharp cut-off point at the Nyquist limit, in absolute terms. In practical terms, the cut-off point is reached before the Nyquist limit. In other words, we're talking about 2 1/2 to 3 pixels per line pair in a Bayer type array.
Lenses do not have such a sharp cut-off point with regard to resolution. They keep on resolving more and more detail, but at an increasingly lower contrast. Even at F16 a lens can resolve 100 lp/mm, but at just 10% of their original contrast.
Since image resolution is always a product of lens resolution and sensor resolution, if you keep increasing one without increasing the other, the advantages in respect of recorded image resolution become less and less relevant. There's a law of diminishing returns at work.
The Canon 100-400 IS is 'out-resolved' by the 50D. It needs upgrading. A good quality EF-S 100-400/f5.6 would be fine .