Pharmacologically I'm not sure how much difference there is between the various colors, although I've heard it said that black is strongest. But I would echo Northape about yellow or Cielo/sky ayahuasca being the recommended place to start. Many shamans/taitas will only work with Sky ayahuasca, saying that black Ayahuasca is for dark magic and sorcery, while Sky ayahuasca is for healing and learning. Take this with as big a grain of salt as you like, but that is what I have heard said.
While I don't have any experience of rue, I would also echo what Northape says about ayahuasca being an intense emotional (and sometimes physical) purgative. More so than any other medicine I've worked with, ayahuasca churns through your shadow like no one's business. This is great if you want to face all your demons. And also understandably avoided or substituted if you don't.