I've owned them both and I prefer SS Joker Poker. Both were designed by the same person, but I think the rules are much better in JP since JP forces shots to be made all over the play-field to do well and there is no way to avoid going for risky shots at times, since the payoff for making those risky shots (e.g., finishing a target set) is well balanced with the risk.

FD, on the other hand, has a rule set with an obvious big points/lower risk strategy that forces one to decide if they want to play for big score or play to interact with the more fun rule-set features. This is a problem I have with FD rules as the coolest task is working towards and collecting the horseshoe targets, but this is also a very risky strategy and it usually leads to lower scores. If you want big points on FD, you generally want to avoid the targets and shoot for the top lanes, top stationary targets and the two saucer holes.

Having said this, I also believe that both are great games, so your decision could also be based on relative price and game condition of the two choices (or, as previously mentioned just buy both).