The XK System is more portable, since it breaks down into four pieces (the top keyboard, the bottom keyboard, the stand, & the pedals). Each piece weighs under 45lbs, so it is a lot easier to move.
The New B3 doesn't break down. It is modeled after a B3 (same style cabinet) so you have the organ and the pedals. Even though it weighs less than a tonewheel B3, it's still a very large piece of furniture to be moving around.
The other difference is that the New B3 has 9 real analog contacts under the keys to emulate the keying system of a traditional B3 (which has 9 busbars). This is where the infamous Hammond "key-click" sound comes from, which is essential to the instrument. On the XK System, the key-click is sampled (although I must say, it sounds damn good... I can't tell the difference).
They make a portable New B3 for $12,000 that is in a sort of metal / plastic type case that is a bit more portable than the all-wood one.
http://hammondorganco.com/portableB3.htm
They also make one with "european styling", whatever that means. I think it's supposed to compete with the Diversi organ.
http://hammondorganco.com/B3ultimo.htm
Pretty neat, but I have no idea how much it weighs, how easy it is to move, or what it costs. Probably not much cheaper than the Portable B3.
For me, the best choice was the XK System.