I think everyone knew Manuel was a project coming in. And I don't think the plan was to ever have him start last year. But then Kevin Kolb got concussed in the preseason and Manuel got thrown into the fire prematurely.
Then this year, all the other QBs in camp flamed out worse than Manuel, forcing them to overpay for Orton to come out of retirement. All the reports have been that Manuel has improved in pra cuticle since he's been benched, but obviously that has yet to be seen in real game situations.
As to why they played Orton instead of Manuel when they " had no realistic shot at being contenders," I feel they actually believed they had the chance to contend if Orton actually provided average QB play. They had arguably the best defense in the league outside of Seattle, and that was with losing their best LB, who will be back next year. Orton actually started out playing well, but turned to crap the second half of the season.
Doug Whaley, outside of QB, has done a very good job building this roster. You can say he overpaid for Watkins, but quite honestly, the difference between what Watkins did and what Beckham did is the difference between an average QB like Eli and a poor combination like E.J./Orton. But he completely fleeced Grigson in the Jerry Hughes/ Kelvin Sheppard trade and smartly didnt overpay for Jarius Byrd. QB and offensive line just have to be the major positions to address in the offseason.