I would like to switch from 13 inch to 15 inch Macbook Pro (both are non-retina) because the 15 inch is 2 years newer and has 16GB RAM. However, I don't want to clone every single thing and I also don't want to lose the development environment setups (XAMPP, Virtual Machines, Eclipse) I have in my 13 inch Mac. What would be the best way to make the switch smoothly without losing these environments that are time-consuming to setup, but also leave behind a bunch of files cluttering up the SSD?
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).