The neuropsychiatric side effects of efavirenz are sometimes an issue with Atripla, so I think Btripla will primarily be used in patients who are intolerant to efavirenz. If I'm not mistaken, the incidence of these side effects are lower with rilpivirine.
The main stumbling block for Btripla will be concerns about its efficacy, so I don't think it will cannibalize Atripla's market share substantially. I don't see it being used a lot in 2nd line if patients have virological failure on Atripla. However, a quad pill with Prezista could be a different story - provided cobicistat's long term safety profile is deemed acceptable. It might cannibalize some Atripla use in first line, but it could provide some growth for Gilead in treatment-experienced patients.
I think the reason why Gilead's stock price has stagnated recently is because its sales for its HIV franchise are not likely to grow substantially. IIRC, sales did drop in the first quarter this year. The quad pill might change this, but I think there will be significant competition from ViiV's own NRTI-integrase inhibitor combo.
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