I'm on the fence with neither.. but a little bit of both.
I run both reef-pi and Apex Classic, and hoping at some point in the near future to integrate the two using the Pi as a proxy (and publish instructions [emoji54]).
There are always tradeoffs... Apex is pretty rock-solid, efficient, stable, great at the low-level stuff.. if it's responsible for the continued operation of a tank with thousands, if not tens of thousands worth in livestock, it needs to be. If something's gone haywire, I want real support with an answer or fix most rickey-tic.
The Pi is not that thing... yet. And it may never be, due to the internal Pi architecture and pile of *ahem* community-supported code *ahem* that is Raspbian (Check out the status of the Vertex Cerebra for perspective).
On the other hand, not having usable analog inputs, BLE radio or legit security hardening on the Apex are unforgiveable and shortsighted.
So... long story longer: reef-pi on top of FreeRTOS, BSD, or WindRiver Linux; running on a Beaglebone (or RPi with Arduinos handling the real-world interfaces); and @Ranjith on the payroll for 24x7 support gets my hard-earned cash.