I have both. I started with the 366 and recently purchased a used 9000.
My pro and con list: I like the size of the 366. I find it easier to get in and around the machine when making adjustments or clearing mishaps. As mentioned above, there will be mishaps and you will need to clean up the machine. The bigger foot print of the 366 also means more bench space if that is a concern. The 366 is definitely more robust, mostly cast parts and the 9000 is more formed and tin parts, making the 366 heaver to move about but very solid.
The priming systems I would call a draw. The 9000 mounts to the side of the machine, on mine anyways, and is actuated by a pull chain. The primer system on the 366 is a tube feed system that is drop fed. I think both could have been designed better than they are. I don't like the pull chain set up on the 9000 and really, how hard would it have been to put a shut off on the 366?
The 9000 deprimes and sizes all in one step, the 366 uses two separate stations to accomplish this, win 9000.
I like the powder / shot delivery systems of both loaders. You can tip the bottles back on the 9000 for removal and emptying, the 366 requires you to remove the top assembly the houses the powder and shot bushing to achieve the same, one thumbscrew, not a huge deal. The 9000 has a system in place for interrupting the component delivery if no hull is present, on the 366 it is two separate manual functions, one for shot and one for powder. I would say the 9000 wins on this one but the system does not always engage resulting in occasional spills, on mine anyhow. The 366 also uses shot and powder bushings that are compatible with other manufactures, the bushing for the 9000 are proprietary although you can buy an adaptor to run MEC bushings in the Hornady machine.
With the 9000 you can easily remove a shell from rotation for inspection at any point. This, in my opinion is the largest draw back on the 366. You must cycle the shells through the entire process to get them out. I have seen DYI fixes for this that involve cutting the retaining ring at each station. I have not done this on mine.
I prefer the wad guide set up on the 366. It swings out for easy placement of the wad. On the 9000 it is stationary and you must slip the wad up and onto the the shot tube to get it into place.
The 9000 sits higher off the bench with a plastic tray that sits under it to catch the spent primers. The 366 has a catch bin that slides in and out formed into the base of the machine. I find the 366 handier in this department.
The shell plate advance for the 366 is a pawl system that is mechanically actuated. The system on the 9000 is driven by a gas filled ram. Both work well with my preference being the 366's system strictly based on simplicity of design and fewer moving parts.
As far as operating the machines, I like the 366 better. The handle is mounted off to the side where as the 9000 is mounted directly in the middle. Once I get set up with all my components on the bench, wad on the right side and hulls on the left, I feel I am constantly moving out of the way of and working around the handle on the 9000.
So, if I had to pick only one it would be the 366. I find it easier to operate with a more robust design. It does, however, have a few things that bug me, no primer shut off and inability to pull a shell from the line at any point.
Just my 2 cents but I hope you find some useful information in the above.