What's the difference between flashing Gapps on system partition vs installing from play store? So I'm finally diving into the custom ROM world after experiencing some issues on CM12.1 on my OnePlus One. I have a question though that googling couldn't answer. If I flash only the essential Google stuff : play store, play services, etc, and then install the rest of Google apps from the play store, how would that be different from flashing the full Google apps package? Apart from, of course, using space that would have otherwise been used on the system partition.

I'm especially interested in this as there are a lot of Google apps I never use. I'm aware of the existence of smaller sized Gapps packages but none have the combination of apps I want.
You can go ahead and flash Gapps Pico (Google system Base, Google play services, Google play store) which contains apps that are essential for Google Play-store support. You can later install other Google apps which fit your need.
You can refer to the image below to find if there is any package that fits your need.


Click to enlarge. source:androidrootz   

Alternatively, if you are not satisfied, you can install the Complete Gapps package and simply uninstall whichever apps you don't need by Root Uninstaller