The most interesting change you can implement in this sequence is the object's TYPE. If you would want to fly an F-15C eagle in USNF/ATF, you'd make a mission called "Eagle" where you chose an F-22. (It's easier to find it if your aircraft is the only F-22 in the mission) Then you'd exit the game (or press ALT+TAB if you have the '97 version) and start a text editor (like EDIT or WordPad). Load the EAGLE.M file into the text editor and find the object section of your aircraft. (The one that contains the line Controller $80.) Change the Type F22.PT line to Type F15.PT and save the file. Now enter USNF and start the mission in an F-15C! (The "Select Plane" screen must be disabled for this to work.)
If you want a real challenge, you can try to set the skill level of your opponents to 4. This should make them really good, but any other number than 0, 1, 2, 3 or 4 will cause the program to crash.
Thanks to Wes "the Sandman" for this tip.