In other cases it might prove more limiting - A Spolite might, during the ongoing campaign findthemselves exiled in Prax and, rescued by nomads decide to join the cult of Waha! to aid their survival in the harsh environment. He might find it more difficult under the latest rules where his Darkness, Law and Stasis Runes have nothing in common with the Cult he wants to join than he would have done under RQ, where you would have just checked that the two cults were not "enemies"...
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There are advantages to the new way as well. In the older rules, a person changing cults would essentially have to start all over, in HQ2 he would simply have to find a cult compatible with his rune(s) and would retain that rating, though of course he would have to learn any specific "break-out" feats.
Also, Waha would be a Spirit Tradition rather than a Divine Cult.
Mark Mohrfield