Given the architecture differences (Atom has 2 integer execution units vs 3 for the Isaiah), the results aren't too surprising. CrystalMark is multi-threaded, so that kind of helps the in-order execution, hyper-threaded Atom compete vs the out of order execution Isaiah core.
The Atom 1.6GHz is a Silverthorne model with a 2W TDP (an Atom 1.66GHz would be a Diamondville model with a 4W TDP). The Isaiah 1.6GHz is a 20W TDP model.
It looks like you will really have to decide on a trade-off. Small devices like MIDs, PDAs or phones won't even use the higher clocked Isaiah models due to the relatively high power usage. Even the slowest LV Isaiah versions use over 2x more power than the fastest mobile Atom models. SFF desktop boards and very small laptops can use either one and power draw will be a secondary or primary concern after performance, respectively.