I bought the 11000SE because of the stippling feature, because I was new to quilting and thought, wow, I won't have to stipple. You really can't manipulate the spacing on the stippling and it's really close together squishing the quilt too much for my taste.
I use the embroidery feature to do quilting motifs on runners and such. Make sure you have a sturdy table to put the machine on when embroidering, because it tends to vibrate(as all embroidery machines do when they are embroidering full speed) so that when the machine runs over stitches more than once they are lined up.
It is a fine sewing machine with all the bells and whistles you could possibly want, and the price has come down alot since a new high end machine is coming out in the fall.
The interaction with your computer and the sewing machine is pretty easy. Make sure you do all the updates from the Janome website. I'd get a copy of the 11000 Customizer program because it allows you to alter the sizes of embroidery files and then send them to the machine. If you put the design in the sewing machine you can only resize it about 10% total. I use the Customizer for monogramming as well as using it to search through all the different subdirectories of embroidery CD's I have on my hard drive. It's really cheap, like 20 bucks, it's discontinued so you can get it on Ebay.
I got the new Horizon 7700 for my everyday quilting and piecing because of the 11" arm space so I don't really use the 11000SE much at all anymore. I found I'm not too big on embroidering pictures on stuff. Oh well.