This is exactly what I plan to do. I already have the 12.9 and the 9.7 arrives today . I think they will complement each other very well with the 9.7 being my main device for commuting, meeting notes, quick reply to emails and refereeing PDFs material. When I require a bigger screen or split mode then the 12.9 will come into play and will be my "laptop device". For everything else that IOS can't do then I would use my iMac when i am at home.
To be honest I do not understand your setup. I have similar needs if I understand yours, but my setup will be:
- IPad 9,7" (to consume media and produce stuff on the go)
- MacBook (on the go, just when needed)
- Docking station including larger monitor, hard drives, connections, etc (for more powerfull stuff at home)
At the moment I still have a laptop plus a Mac mini, but I plan to merge them as soon as apple will merge USB c with thundebolt as I plan to purchase an external graphic card.
Not quite sure why would I need a 12.9 iPad?
By the way, a mouse would be very appreciated on the iPad because with some clients I need to use Citrix on the go and it is quite painful without a mouse and I have to switch to the laptop.