Bear may have some comments, since he has lots of experience with various MES units.
I have the MES 30 and my personal experience, which is confirmed by what I've read, is that it has all sorts of hot spots, not just top to bottom, but left to right and front to back as well. Mine has both the heat source and the exhaust on the right side, which creates a heat flow up the right side, so things on the right get cooked more.
Some people have created all sorts of mods to force the heat to flow to the other side, eliminating the hot chimney up the right side. My solution is simpler: I rotate the racks top to bottom during a long smoke and, when I do that, I also rotate each tray 180 degrees (i.e., front to back). That seems to pretty much take care of the problem.
[edit]Shortly after I posted, I thought of another variable: the water pan. Most people don't put water in it, but some people fill it with sand and then cover it, thus creating both a heat sink, which buffers temperature swings as the heat cycles on and off, and also a heat buffer, somewhat shielding the lower rack from the heating element's radiant heat. I've never filled my water pan with sand, but if you can be certain that the sand is inert (i.e., won't give off fumes), filling it sounds like a good idea.