I would forget about using 25mm for the side plates, mine are 12mm and are extremely solid. The entire gantry is only bolted together with 8 M8 bolts and there is no deflection (I can put my foot on the top corner of the gantry and push with all my weight and there is no detectable deflection). 25mm would be very very heavy.
My thoughts against MDF are that it can distort when bolted down and any moisture would cause problems, it would also not add any rigidaty to the frame. If I used a aluminium plate I would skim this, maybe a couple of 5thou passes. The problem with this is that my table will be bigger than my cutting area so skimming will result in a recess.
Sizing steppers is hard as it depends on what screws you use and the speeds you want to run at. My opinion is the bigger the better.
Thanks for the comments, hopefully I will be cutting in the next couple weeks.