I believe Honda have faith in the future stars that will be in the Repsol garage in 2006. They are holding out hope that Hayden will fill the bill that came with him in 2003 and there is a lot of faith and expectations in Pedrosa. Better to put it into two young riders than riders in their 30s.
As far as who could get the factory Yamaha ride alongside Edwards, Hopkins would have most likely been a candidate, Jeremy Burgess has said there are teams in MotoGP interested in Casey Stoner so he must be a candidate. And just to throw a wildcard into the mix I would look to... Kenny Roberts Jr. (gasp). He has had a dismal past 4 seasons but they have all been attributed to an underdeveloped motorcycle and lack of motivation. Put him on a Yamaha and you have to believe both of those problems would be solved. It's a long shot but it may be worth the risk of a one year contract.
Marbles, I haven't heard anything about Yamaha having any offers on the table to Gibernau so I don't think it is very likely but a possibility none the less. Should Rossi leave for F1 in 2007 as is rumored, Yamaha will be looking for another top rider (especially if Edwards can't run up front more consistantly) and if they already have the services of Gibernau enlisted then that rider search is done.