The main thing Area 69 had going for it was the
sexual reference in the name underground, the 'secret' part of it, however there is only limited things to see there, but the mission there was one of my favorites, especially trying to creep around stealthily without being noticed. But in terms of layout/content it wasn't much like a major army base (which it would be as its the only one in San Andreas).
Zancudo on the other hand had the perfect layout, content (jets, jeeps, trucks, tanks, helicopters, titans, marching soldiers, a full runway, storage areas, fuel tankers etc.) Every time I enter Zancudo it's thrilling as you don't know whether it'll be a tank, soldier on foot or someone in a jeep that will come after you and it's a challenge to get out of there once you've gotten what you came for.
For me it has to be Zancudo, but I did love Area 69 in the days of San Andreas