Yes, versions of the JSF are also going to be sold to allies. But that only underscores the apples to oranges comparison. It's not just about cost overruns -- if it were, the Navy wouldn't have nearly as many ships. It's also about mission requirements, how good the platform is at fulfilling those requirements, and where our senior leadership thinks the threat is going to be in the foreseeable future.
Aside from the fact that each airframe exceeded budget estimates for different reasons, senior USAF leadership couldn't convince SECDEF Gates and Congress why it needed to continue acquiring more F-22 aircraft given the current and near-mid term threats. Also, if the need arose, the F-22 could be put back into production, and hopefully not peacemeal over 46 states.