After playing both of these machines at the Pacific Pinball Museum yesterday I decided that if I were to buy one of these machines it would be Funhouse. Overall I just like the art and lit feeling of the game compared to the BSD. Also Rudy is a great aspect of the Funhouse as well. I must admit that someone who is really good at pinball might be better adept to enjoy one game over the other, making one a clear choice for them. I can see where both games are sought after but in thinking about it I will go with neither right now. Neither theme really hit home with me, at least enough to justify a used one of these as my #2 pin.
With IMVE coming out I think my money with a little extra padding is better spent there in my particular situation.
Thank you Pinsiders for your great advice! I really appreciate all the insight that you have provided.