Though I really don't know much about Aiki jujutsu, I know Small Circle uses two lever action instead of one lever to make the technique more "efficient." Heavy emphasis is placed on attacking the tricep tendon(rather than elbow), especially in standing arm bars. The wrist is usually flexed to add more tension as well. The same wrist extension would be used in a leg bar as well against the achilles tendon. Another example would be in the rear naked choke. In SC the wrist is placed across the larynx/windpipe, and then flexed into the area while applying the choke. I know in Brazilian/Gracie Jiu Jitsu, emphasis is placed more on centering the elbow into the front of the throat and then applying pressure on the carotids. SC also has several finger locks which can't be applied in a tournament setting, even UFC styled.
So basically in SC JJ:
two lever action
small circle extensions(like the wrist extending)
many moves attacking elbow changed to tricep tendon
I'm sure there are many other differences, but since I don't know anything about Aiki JJ, I can't really differentiate for you.
There's a couple of videos on youtube with Wally Jay, but I think they are just finger locks, still cool though.
Well if your Aiki Jujutsu is anything like mine, you will find many similarities with SCJJ.
I've crosstrained with Bruce Chui,SCJJ 6 Dan, a good bit, and they dont upset each other. It tends to give you a few new tricks and looking at things from a different perspective.