Both are good units, but the 9000 has automatic shutoff for the powder and shot, better (collet) resizing, one less move for case resizing, and cases are removable at every station. Also, the automatic/independent indexing (gas piston) on the mec is superior.
If you don't mind resizing/depriming all of the hulls a separate operation before reloading, the 366 becomes a much smoother machine. Get the new style 366 spring-type primer seating ram. The 366 also prefers hulls in "good" condition, due to the swinging wad guide thinner petals. The 366 has a better primer feed system, and the entire machine is much more stout.
Parts availability is good for both machines (internet), but it seems more shops stock the mec items, as it is a more popular, better selling line.