Welcome to Chicago, Happy Camper.
I, too, often dine alone, both because I travel a fair bit and because I sometimes want a good meal without having to "arrange an evening" with someone. I've found that most places are becoming accustomed to women dining alone -- or solo diners of either gender. Sometimes, other solo diners are on their own because they're from out of town, but I can remember being at Alinea once when we noticed a lone diner and, being in a merry group, we asked our server if the lone person would like company. We were told that no, this gentlemen came often, always alone, because he wanted to focus on the food, not on people or conversation. And they were cool with that.
One of my favorite "hang outs" is a fairly high-end place out in the suburbs (not in the city, as you specified, but used as an example). Le Titi de Paris has a great $16 fixed-price lunch, and I'll often go, curl up in a booth, and read a book. After I've enjoyed my lunch, they'll keep on refilling my iced tea for as long as I stay, which has sometimes been a couple of hours.
But I've found that just about everywhere I've been, I've had no problem at all dining solo. However, I have had situations like the one in the thread you reference where I waited for far too long (sometimes after asking several passing staffers where my wait person was) -- but that was actually when I was with someone, or even several someones, and not alone. So I'm not sure being overlooked is really necessarily connected to dining solo.
I'll leave the general urban recommendations to the group's city-dwellers. When I'm in the city, it's usually for high-end or funky ethnic, so not much of that "in between" stuff to recommend, at least not in the seafood-dominant category. But I haven't run into any real issues with dining alone anywhere. Though I do always take a book -- just to fill in those time gaps when service is slow.
So I'd say just search the site for places that sound good to you, and check them out. If for no other reason than the fact that this is a huge convention town, most restaurants are cool with lone diners.