Very small polys typically occur only in quad meshes. In the tri meshes MD uses natively the size of the polygons is much more uniform. Quads are recommended for long narrow panels that are primarily bent along an axis perpendicular to the long side, say straps and ties. I have been using MD since MD2 was released and I cannot remember a case where I saw a reason to convert a main garment panel to quads. 

The long narrow facets may occur in piping. Best define these in MD as a separate material so in the cloth room you can easily assign the vertices to a soft decoration group.

I found 'non-manifold' meshes may simulate well in the cloth room, but mileage varies. The cloth room is not very good in handling layers that are colliding, and unless the cross section of the 'junction' has a clear 'T' shape you easily end up with colliding layers. If there are (quads!) very small polygons near the seam, the boundary conditions may soon become conflicting and results become unpredictable.