I always preferred the Cobra Temples, myself.

The temples gave variety. Consider:

original Cobra Temple: ARAH 1-3 and 5
main Cobra Temple: TROC parts 1-5, Battle for the Train of Gold, The Funhouse, The Traitor I-II, Eau de Cobra.
Temple Alpha (same place?): There's No Place Like Springfield I flashback
waterfall Temple: TPOD 1, 4, and 5
snake-head desert base: Cobra Soundwaves, The Greenhouse Effect
ziggurat training camp: Countdown for Zartan
Patagonia snake tower: Cobra Stops the World
riverside base in India: Jungle Trap
Cobra/EE headquarters: Red Rocket's Glare
Rocky Mountain temple: Money to Burn
Easter Island training camp: Operation Mind Menace
South American temple: The Funhouse
And over 40 other bases in the first season

Most of these ended up evacuated or destroyed by the end of the episode; lots of fun there.

Then in the second season we have...Cobra Island with its Terror Drome. Yep, that's about it for the second season. Joes slipped in and out but rarely staged any sort of assault. Cobra was usually defeated long-distance. Oh, and there were a couple other bases, but nothing like the variety we saw in season 1.