I run Aperture 3.6 with OS 10.11.4 (El Capitan) on an iMac and with OS 10.10.5 (Yosemite) on a MacBookPro. I find significant differences such that I much prefer to work on the MacBook.
(1) with Yosemite you can select a set of images and add a keyword to all of them at once, either by dragging the word from the Keywords list or by clicking the word on the Keyword Control at the bottom of the screen. Or from a selection in the Metadata menubar.
With El Capitan I only can add a word to one image at a time with this method, no matter how many are selected. What I have to do is use the menubar pulldown Metadata / Batch Change and, under Keywords, type in what I want to add
(2) with Yosemite I can plug in an SDCard from my camera and be asked to import all the photos on it. They will be broken into sets by date.
With El Capitan the card will be recognized, but only the last dozen or so images will be recognized. If I have more than that small number of photos I must drag the icon of the photo folder onto the upper lefte of the Aperture window. All the photos will be imported, but in a single project. I have to separate the dates, one by one, by creating a succession of new projects.
These are not showstoppers for me, but they are sufficiently annoying and time consuming, compared with what I was used to, that I would recommend not upgrading to El Capitan.
I had thought to create a Yosemite startup drive, an external drive that had Yosemite on it, so that I could run Aperture on the larger-screen iMac. but the installer I have will not run on the iMac and the Macbook says the installer is damaged. The Apple App store knows I have downloaded the installer, so neither Mac can redownload it.
I cannot figure any way to get an external drive running Yosemite that I could boot from when I want to work wotjn Aperture on my iMac.
Hence my advice against upgrading to El Capitan if you use Aperture.