I think the standup quilter is easier for some things like keeping the quilt flat etc.
The sit-down quilter IMHO gives you more control. You can turn the quilt whenever you want so that if you can do feathers better in one direction, you can always do them in that direction, etc. You can stitch a long line in one direction.
I have a standup. I'd love to build a sit-down table for it so I could do one or the other depending on how I feel.