Currently when you open a Site Analysis report it populates it with the most popular pages (along with a few other rules).
If you then apply a segment to that, you see the same pages but for that segment.
That doesnt work so well when you have a mobile site, and add in the Visitors from Mobile Devices - it doesnt auto-pick the pages that mobile visitors went across. It's the same pages as All Visits. You have to then manually add in your own pages, and you're therefore not seeing the true picture and quite possibly missing an opportunity or an insight.
If you had the option to apply the segment before the "auto-pick startup rules" were applied, then it would pick the top pages (et al) based on the new segment, which would really enhance that report.
Not just for mobile either - every single segment has different behaviours and the Site Analysis would be much more usable if it based it's display on the segment. Of course, as we want our cake too, we want to be able to optionally re-cast the view of existing pages from the existing segment (likely to be all visits) based on the new segment as well...without changing the old pages.
So, we want it both ways, but if that's not possible to have both ways, then the segment-based way is best (IMHO).