Well I ended up returning the 12.9 and got the 11 instead. Was a bitter sweet decision that, like many of the posts above, I knew it was the correct decision for my use case.
I wanted to get on with the 12.9 more than I did. When the 12.9 is used for viewing videos (from a reasonable distance) and using split screen apps it is an exceptional device. The screen and sound quality are a true upgrade from anything I have experienced with iPads.
The 11, to me, feels more incremental of an upgrade in comparison. I think my opinion is tarnished by using the 12.9. This is not to say I am down on the 11, it is a wonderful device, but it feels less of an upgrade in comparison to the 12.9.
When I compare the 11 seperately to 9.7 / 10.5 it is a nice, albeit modest, size increase. Also the black boarder issue on 11 is making the device seem smaller than it is, hopefully updates start coming through this week. This was noticeably less of an issue with the 12.9.
The fact remains that when I grab the 11 for whatever my needs it delivers. This just wasn't the case with the 12.9, it was just a bit too big and unwieldy for the majority of the time, and the few occasions when the size wasn't an issues it truly excelled. As with the analogy above, the 80-20 split couldn't be justified.
I hope at some stage Apple move to a 12" tablet, this will be the true sweet spot for me.
Thanks for the opinions people have shared here, it has helped me bring into focus my own thoughts on the issue by listening to others experiences.