Sounds like Disney really mismanaged this.
When I arrive at WDW after a day of traveling, I just want to quickly check in, drop my luggage in the room, and get to a park. I would be extremely annoyed to be told at the front desk that the room REALLY isn't ready and that either I can take two rooms instead of the suite or go across property to check in to a suite at Fort Wilderness or Saratoga Springs. Whether you consider either of those an upgrade or not, the change of resorts would take away precious time in the parks. But whoops, "We didn't know until this morning the suites weren't completed," thus we couldn't warn you before you got here.
I would be fuming. Not a great way to start a vacation.