So here's why... (I think... it's close, but any electricians out there feel free to interject...)
Each solar panel is made up of a multitude of cells. Each cell produces about 0.5V, so a 12V panel normally has about 36 cells wired in series - to give a charging potential of 17V. Amps are generated according to the amount of sunlight - but following Kirchoff's laws for a series wired circuit, the current in each cell is the same. If you short circuit one cell, you effectively short circuit the entire cell. Output drops to zero. If you use the same shade area but apply it at the intersection of 4 cells, partially shading them all, the reduction in output will be less marked since only 25% of the area of each was shaded...
For a 12V system, with 2 panels, wire them up in parallel so that if one panel is shaded, output from the other will remain good. If wire in series, than shading of just one cell of the two panels will kill all output.
If you were to wire up 2 in series, you'd end up with an output voltage of 34V - wouldn't that harm the batteries? Just how smart are the solar controllers?