I understand your logic and I agree with you but that is why we use directional powerheads, such as koralia 1/2/3/4/5/nano. The water flow from these stirs up the muck and that in turn gets drawn in by the weir.
The water going over the weir will have heavy flow of its own due to water falling over it, in fact my one is drawing water in at around 1100gph (~4100 l/h) which is equivalent to a very large powerhead. It is just a matter of kicking up the muck to get caught in this flow.
Placing an intake low in the system presents problems, the way around this is to place the pipes in an upside down 'U' with a hole drilled at the bend at the top to act as a syphon break should the pumps fail. This would allow water to be sucked in the bottom without fear of emptying your tank in a pump failure.
However, I think the poor aesthetics of this would outweight the benefit if it was not hidden behind a weir, which defeats the whole purpose of it. Plus emptying sand from your tank would also be a huge negative, with a weir the fish would have a hard time kicking sand into that flow.
I have no experience with this though as I operate a weir system so I am sure someone who has done what you have suggested will chime in with better answers for you. These are just my immediate thoughts on it.
http://www.monsterfishkeepers.com/forums/member.php?u=32235 This mod, Pharaoh, will likely have better answers for you than myself.