How do I perform a partial clone between 2 MacBook Pros?
I would think that the easiest way is to use the Migration Assistant to copy your user account from the 13" to the 15" MacBook Pro.

This would ofcourse copy both the stuff you want to hang on to, and the stuff you don't want to hang on to. After migration has completed, you will need to delete the stuff you don't want.

The 13" MacBook Pro will continue to work as before - you will not loose your development environment there.

The only real alternative to this is to manually copy over only the bits you want - I'm guessing that it is much easier to delete what you don't need instead.

Also remember that with SSDs small files "cluttering" the drive is not the same technical issue as it could be with hard drives (i.e. fragmentation, etc).