higher clocked processor in the 12.9 is barely noticeable in the real world usage. The 9.7 has less pixels to drive so it's pretty much the same in that aspect. The camera, true tone feature and screen is better on the 9.7. I had the 12.9 but sold it to get a 9.7 as I find it much better overall.
That is a common belief (12.9 has more pixels therefore more RAM is required) and it is true to a certain extent. The 12.9 doesn't have 2x the number of pixels and not all RAM is used for caching video/screen. As a result, there is more RAM "headroom" on the 12.9 compared to the 9.7. It is not "pretty much the same".
For you, the camera and true tone features were more important than increased clock speed and RAM. That doesn't make clock speed and RAM of no importance... in the same way that RAM (and to a lesser degree, clock speed) are more important to me than the camera and true tone... but that doesn't make them of no importance.
Another difference is that on the 12.9 iPP, split window results in the full presentation of each app in the window. On the 9.7 iPP, it displays a simpler (phone) view of each app.
I initially held off on buying the 12.9 Pro to wait to see what Apple did with a 9.7 Pro. When the 9.7 iPP was announced and I learned that it had only 2GB RAM, it made my decision easier to go with the 12.9 Pro. I wanted a device for the long haul and the greatest indicator of longevity is RAM. I always buy the iPad generation that initially bumps up the RAM (only exception was the iPad 1 which had no predecessor).
I've purchased the iPad 1, iPad 2, iPad 4, iPad Air 2, and 12.9 iPP. That has worked out extremely well for me.