Dealer prep or other adjustments will not make the hitch smooth. It is not designed to be smooth. The response I got from my regional Kubota rep was that the value tractors (Standard L's and MX's) are not engineered to have a smooth hitch. If you want or need a smooth operating hitch, you will need to purchase a Grand L or M series Kubota.
I can't say anything bad about the MX5100 otherwise. It provides a lot of tractor and power for the money, just depends on what you are looking to use the tractor for. If you plan to do any grading, use a PHD or any other implement that would require fine control over the 3PH, then you will not be happy with the 3PH performance. If not, you will not even notice the jerky hitch. It is smooth when raising quickly, just can't feather it up smoothly.
I returned my MX5100 after 2 weeks and purchased a Grand L 4240 because I needed a smooth hitch for grading. Couldn't be happier, it was the right decision for me. If you will mainly be doing PTO or FEL work then the MX5100 is a great choice.
Hope that helps...