I consider the CC 2015.3 update to AE to be like CC 2016. It's a separate app that installs alongside CC 2015 IF you uncheck the box in the CC app before the update (under advanced options) that removes old versions. (Details about that tricky box here.)
It's a bit of a hidden option, but you can install CC 2015 (as well as CC 2014, CC, and CS6, if you want) via the Creative Cloud app (and, if you do, it might help you find your missing plugins) - details on installing old versions here.
If you use Spotlight to search for After Effects, does it give you any indication where it's hiding?
Try using Spotlight to find your old plugins and scripts folders. Since CC 2015.3 is a separate version with a separate install location, you will need to copy those over to the new version just like you did for CC 2014 to CC 2015. You may even need to get updated installers for some of your plugins. Red Giant, for example, has new installers for some of their plugins that need it.
When I did the install it said it was a 2015 update and not a full version 2016 update so I did an all install. I never do a full version update unless its tried and true. And yes I did a computer wide search and found only the uninstall programs. Makes no sense to me.
I guess my only course is to spend the time and reinstall the older version of 2015 along with all the plugins & scripts. Such a waste of time.
When I did the install it said it was a 2015 update and not a full version 2016 update so I did an all install. I never do a full version update unless its tried and true.
You're not the only person to think that. I've heard from many others about this. If I could find whichever Adobe executive decided to go this route with the naming (and having CC default to removing old versions), I would give them a piece of my mind, bless their heart.
You can't even find the old plugin folders, huh? Darn.
You might just install your plugins and scripts anew and not worry about the older version(s) of AE unless you hit a bug or something. I actually quite like AE 13.8 (AKA AE CC 2015.3) despite its awkward naming.
Thanks for trying...I would leave the new version but I don't even know where its installed, nothing shows up in my applications folder.
How do I tell the creative cloud app to install the software where I want it on my Mac drive?
I had the same experience when updating. All my plugins and scripts was deleted from After E. (OSX El Capitain). Fortunately it looks like Adobe kept a folder next to the new "Adobe After Effects CC 2015.3" with my user installed plugins and scripts, so they were easily reinstated for me.