I admit I'm spoiled by the simulator at The Experience but the bigger shuttle seemed like a mall ride (fairly mild) and the interior is not "dressed" at all. The smaller one is better for the motion experience but you can see the Windows Media Player skin around the graphics. Lame. The graphics themselves (and in Long Beach both simulators used the same sequence) seem very mid-level video game to me. Since I believe it's still included in the ticket price, try them but I definitely recommend lowering your expectations.
I will say that I think smaller may be better with the exception of the loss of the Ent-D bridge. Also, in Long Beach, they didn't do a lot with the Quark's Bar material; it just kind of sat there. Again, I'm spoiled by The Experience.