I just read a review for the new wavelab 8. It has a new feature, which allows you (as far as I understand it) to combine multiple clips, to work on them like on one clip. So far so good - just export stems you say? But the trick is, that you can go back into the single clips and edit them again, without the top-level-processing being lost. It reminds me of the way you work with sequences in Adobe Premiere.
My suggestion for Reaper is:
It would be super-duper cool, to be able to open several whole projects (!) as new clips in another project. So you could then again arrange them - make transitions - apply mastereffects in reconcliment - change length (move edges).
Of course you also could bounce every single project down and arrange all the files... But then - for example if you're working on a transition - you would have to switch back into two projects - editing - bouncing - arranging - checking - editing again...
I hope you understand waht I'm thinking of.
I hope this request is not too difficult to implement - but fear it is
Here's a scetch: