the problem i most often run into regarding the mesher is it creates long skinny triangles when i wish it could just do quads.. (those triangles can have weird results in my renderer/textures)
for example, the unjoined surface on the right is how i wish it would mesh that section even when it's a polysurface (left)..
i imagine it's a bit of a nightmare to try to make a meshing algorithms that works right* for all/most occasions.
*with 'right' being a particular user's expectations.
(that said, i can get more usable results than this with different settings.. not as clean/low-poly as the version on the right but still, better)