My greatest design pet peeve is "push" doors that look like they're "pull" and visa versa. You should intuitively know what to do just by looking at the handle. Of course, this is not airport specific.

For airports, most design flaws are inherent in the fact that the airports were designed before "modern" times and modern problems. Capacity is the biggest issue, but also larger security zones, etc. (Unlike one above poster I like security to be right away since my anxiety level goes way down after I clear security).

The biggest airport design flaw that I can think of is that it seems that airports, in general, weren't designed for people lugging baggage. Restaurants and restrooms are especially awkward with a carry-on and a computer.

As for airplanes, the functional design is generally quite good given the inherent constraints (interior design is another matter). One thing I would change would that seats should be designed so that when you recline you take away your own legroom rather than the person behind's. (That is, the seat bottom should slide forward.)