The Federal Aviation Administration's air traffic control system is almost everyone's favorite whipping boy for everything bad that has happened in the air in the past year.

Political pressure persists for rehiring some of the 11,400 controllers fired by President Reagan when they struck illegally in 1981, and FAA chief Donald D. Engen continues to resist it.

Despite some close calls and a highly publicized New York-area midair collision that involved controller problems, the folks in the air traffic office are smiling these days about what they regard as a pretty good year for their performance.

Early statistics for 1985 show delays in scheduled flights were down 18 percent from a year earlier, traffic was up 3 percent, and controller errors down 25 percent.

Another perennial transportation syndrome: When it comes time to negotiate international aviation agreements, both the Transportation and State departments have major roles, with the result that there is a revolving door of sorts between those departments.

Jeffrey N. Shane, recently deputy assistant Transportation secretary for policy and international affairs, took the job of deputy assistant State secretary for transportation affairs. He is the second consecutive person from Transportation to move to that position. His replacement at Transportation is Vance Fort, who was director of special programs for Transportation Secretary Elizabeth Hanford Dole.