The pontoons were used at Harper's Ferry after Antietam. The bridge simply wasn't ready.My understanding was that there was a delay in the pontoons because of a number of SNAFUs about proper transmission of orders - McClellan wanted them at Washington, but the order wasn't sent on from Washington by telegraph and so there was a multi-day delay in their arriving at Washington.
As for Burnside's original plan, I'm having a real job of work trying to work out what the hell Lee could have done to prevent it! (Lee did too, which was why he elected to pull back to the North Anna.)
Halleck, then Lincoln supported Burnside's plan, but only if he moved quickly. I can't figure out why Burnside changed it.