Linmar, I do believe that the Janome has a larger throat space than the Juki, you didn’t mention if that would be a factor. But the Janome is a heavy machine and didn’t come with a case, I really dreaded hauling it out and setting it up, but since you will have a dedicated area for it you should be fine.
The Juki does come with a very nice case, I purchased my Juki from All Brands as a show model and they included a 10 year extended warranty on it as well, everything came in the original box and I was very happy with it. The extended warranty on it means the technician comes to my house to service it which is great!
I agree with Quilte, if your set on a Janome, go with the 6600, let us know which you decide on, it is difficult to choose!