I plan on picking up Handi Quilter Simply Sixteen little foot system today after spending time trying out various sit down and standup systems. I too found quilting on my sit down domestic machine placed a considerable amount of pressure on my shoulder and neck. I have done various size quilts including a King size quilt on a Viking 118. Last year bought a Babylock Jazz - yet, despite it having a bigger throat, I still found myself itch shoulder aches and pains.
The system you chose is a personal decision. For me I found standing up gave me the ability to be much more relaxed that produced better designs - almost becoming one with the machine. Space was an issue so I went with the Little foot system. I also liked the fact it did not have a foot pedal. I found systems with a foot pedal was trying to tap your head and jump at the same time. Lol Try out various models and find the one that you feel you have more control with.