I have no hesitations in saying that you should do the very nice honeymoon. When we stayed for our wedding, we were there for 10 days. It was FABULOUS! we made sure we did lots of things and to be honest, we remember the days of visiting more than the wedding. My thought is that the VR would just be one day-maybe only 1 hour of the day. Just think what that 3000.00 hour could buy over the course of an entire stay! I think the VR at home might be more intimate, more relaxing and could save you money even-that you could, of course spend in WDW!
Now, the only thing I am thinking is: were you married in WDW? It is an experience that is very cool and I can understand why you are considering the VR, especially if you have not had a wedding at WDW.
The choice is up to you, of course, but that stay you described sounds exactly like the stay I am wanting for one of our anniversaries! I think I just talked myself out of doing a VR at Disney and instead staying a very long time and having a blast!!