One thing I always ask myself, thanks to being in the world of IT and dealing with edge cases, is "How would this work across every culture?". - In the case of middle names, there are some cultures that don't have them, and some have multiple, and airline systems have a hard enough time transmitting middle names as it is. Is the TSA going to start rejecting everyone who has had their ticket issued by another airline where their first and middle names are combined into one field, or the middle name field is otherwise empty (or when your prefix (Mr/Mrs/Dr/etc) is appended to your first name)? I find it hard to believe that they would want to do that, especially for the bad publicity they already get.

I also wouldn't worry what is and isn't printed on the boarding pass, as TSA read the data off the barcode, if they even bother to scan it at all these days.