It might be too early, but my hunch would be that everyone wants the hardware specs of an ipad with the form factor of the mini.
If I were Apple and knew this, I would keep them separate just like I do now with the Macbook Pro line with and w/o retina.
You're essentially carving out a niche from that niche. The tablet niche carved itself out with the ipad and now the mini carved itself another niche from that.
From a profit POV, I would imagine companies using the ipad while home users playing w/ the mini. Just like a Macbook Air for personal use and a Lenovo Thinkpad for work.
By keeping the hardware specs ahead of the mini, it will capture and cater to those more pro/powerful (such as designers, engineers, academics and such). The mini would be for more casual use and cater to hungry readers etc.
I believe the profit margins for keeping them split is greater, but it also presents itself w/ a lot of other challenges, inside and out. App developers, managing functions/features across multiple hardware devices, etc.
Bottom line is, I think Apple is waiting to see if the whole power/casual user theory will pan out. If it does, they will keep the two pads. If the mini crosses a threshold of cannibalizing the iPad into extinction, then it's obvious.