Equipment substitutions happen.

I imagine there were eight revenue First / Business passengers and UGS/1Ks flying on higher fares then you and your wife, which is why you were downgraded and those eight were not.

I'd consider an upgrade cert acceptable compensation, since it covers the "loss" of the upgrade you used your SWU on - so no net loss of upgrade to you.

In similar situations, UA has been nice enough to allow me to take a flight leaving close to the time of my flight that had NF space available, but this mainly works only between hubs where you have a lot of flights.

So I think UA went beyond the "call of duty" for you, and that's good for both them and you.