The MX5000 is larger, a little heavier, more power, has a better tranny, more lift capacity for a loader. I would get the MX 5000 if you have a good bit of land.
People say that the L4400 is the most bang for the buck with Kubota, but the MX5000 really is. Quite a bit beefier, almost 15% more hp and bigger loader, the one I looked at had a quick dettach bucket. Pricetag was about $2,000 more. If I had bought new I was leaning strongly toward the MX5000.