When we are doing standard transformations in a 1.5 ml microfuge tube we use two tubes opposed to each other so they knock into each other. This helps dislodge the pellet from the wall of the tube. For large scale transformations try and get vigorous mixing with the tube at an angle so that it also vibrates as well as mixing. Wolfgang Lankes from the Max Delbrueck Center for Molecular Medicine , wrote me with a good solution to the resuspension problem. He uses a rough surface such as a wire test tube basket to quickly run the end of the tube over a couple of times.
Transformation efficiency has genetic variables.
There is dramatic variation in the transformation efficiency of amoung strains currently being used in the general yeast community. Not all strains will give 3 million transformants per microgram of plasmid DNA even if you optimize all the variables. It is best to start with a good transforming strain and then optimize. Cell Growth is very important. Cells must go thru at least 2 divisions before they become fully competent for transformation.