If you own both Prophecies and Factions, and merge them to one account, then your Tyrian characters can travel to Cantha and learn skills there from trainers or quests or captures like normal. And vice-versa for Canthan characters.
If you don't buy Factions, then you can't learn Factions skills. It may seem unfair, but owners of both games are still limited to 8 skills at a time, so it's not really unbalancing.
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