I have an HR21 on my Mits RP. it's native resolution is 1080i. That's what I have my HR21 set at.
On my other plasma display it's native resolution is 720p. that's what I have my H-20 set at.
The native setting on the boxes to me, is irritating, it works just fine, I just don't like the lag in the picture as it resets the resolution.
As far as Stretch, crop, pillar box. Right now both of my displays are pillar boxed for non HD programming. Fortunately with all the HD being provided it's not really much of an issue.
It's a personal preference. My brother can't stand seeing the black bars and stretches whatever he can.