I think that'll probably come down to personal preference and condition. I personally like the look of the 1200 a little better, but when I went shopping for mine I would have taken an 1100 if one had been available. I think the 11 would be easier to convert to a standard model if you so wished? I would take a look at the buyer's guide Steve put together on this forum, it has a lot of really good detail about the different models. I used it as a checklist when shopping and I got a heck of a bike because of it.
I have both a 82 1100I and a 86 1200A. To me, the 1100 is a little more sportier than the 1200 versus the 1200's soft comfy ride. The 1100 is more like an old bike with it's dash layout versus the 1200A digital dash. The seating is also dirrerent. Try sitting on each and your might get a better feel of which you like. One caveat, the 1100 is impossible to get new parts from mother Honda. You are limited to used parts., but it wont be long before that's the 1200 also.
I was just ok with the fairing on the 1200 at first but it's growing on me, kind of angled out like a shark.
As far as the seating position being different, they both seem fine to me.
My first bike was an '88 Ninja then an '81 CBX then a '95 Magna so seating on those were very different and I was fine on all. Still got the CBX. Later.