I am the author of GPEC. Thanks for using our plugin.
For your questions:
1. AUC = 0.67 can be considered acceptable value, since the random value will be 0.5. The AUC value generally depends on how much close to each other in the network genes associated to a disease are.
2. Therefore, if you want to improve the AUC value, you should use more dense network where genes associated to the same disease are expected to be close to each others. For this, a functional linkage network should be used.
3. You are right. Actually, RWR algorithm (the base algorithm of GPEC) is biased to hub genes (high degree genes). Fortunately, disease genes are naturally located in hubs in interaction networks and genes associated to the same disease usually form a so-called disease module.
Hope this helps,